Protein Shop Help!
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John Dohnal
Sep 19, 2013, 8:46:59 AM9/19/13
to diy...@googlegroups.com
I have never used a Linux OS before, but I downloaded the latest version of Ubuntu in order to run Protein Shop. I downloaded the latest version of Protein Shop, but I don't know how to start it. I know nothing about using Linux, so any explicit, basic instructions would be most helpful. In the readme file, it mentions some other files that may need to be installed, but I don't even know where to begin. Please help!
Thanks,
John
Cathal Garvey
Sep 19, 2013, 3:27:26 PM9/19/13
to diy...@googlegroups.com
PS if anyone out there with C++ wizardry skills can get this to compile,
it'd be awesome if you could make a statically compiled version for
John here and others? I'd be happy to host a big honking binary on my
site to make things easier..
Also, forgot to mention that in the makefile on Debian you have to
change the install directory of FLTK from /usr/local to /usr..
Yay building software!
it'd be awesome if you could make a statically compiled version for
John here and others? I'd be happy to host a big honking binary on my
site to make things easier..
Also, forgot to mention that in the makefile on Debian you have to
change the install directory of FLTK from /usr/local to /usr..
Yay building software!
Cathal Garvey
Sep 19, 2013, 3:29:09 PM9/19/13
to diy...@googlegroups.com
Lol, ignore last message a minute, the preceding message failed to
deliver because Google Groups didn't like the attachments. Will post
later.
I'm afraid it's bad news, John; ProteinShop is either a very buggy or
very outdated codebase, and won't compile for me. Perhaps someone with
better C++ chops can pick up where I've left off and make it work.
deliver because Google Groups didn't like the attachments. Will post
later.
I'm afraid it's bad news, John; ProteinShop is either a very buggy or
very outdated codebase, and won't compile for me. Perhaps someone with
better C++ chops can pick up where I've left off and make it work.
William Heath
Sep 19, 2013, 5:27:04 PM9/19/13
to diy...@googlegroups.com
Hi All,
I used to teach c++ and programmed in it for over 5 years etc... I also specialize in linux. I will see what I can do :>
-Tim BCSE, MSCS, MBA
Cathal Garvey
Sep 19, 2013, 6:46:48 PM9/19/13
to diy...@googlegroups.com
Hey Tim!
Below is my original mail outlining the progress I made before losing
heart. It refers to "attached", but here's a link instead to the
archive, as I can't attach it through google groups:
https://anonfiles.com/file/a4c961f31541d7f38575c534ff20a5d1
(Yes, a zip rather than tar.gz, because bizarrely anonfiles.com doesn't
like gzip?)
--- Original Message ---
Hey John!
Welcome to Linux! Sorry you're having trouble already, but looking at
Protein Shop, that's not surprising. I tried to come up with a
comprehensive guide to getting it running, considering that the
developers don't offer compiled programs but rather only the source
code. Worse, it's got big dependencies; OpenGL and FLTK, plus others.
That'd be ok if it was pre-built, because you could just install OpenGL
and FLTK afterwards, but you need to install the "dev" versions of
those, and then build this.
So I tried. I installed all the dependencies and wrote a big email
explaining how, then downloaded the source code, uncompressed it, and
tried to build. Then I found that the source code bundles "Geometry"
and it doesn't compile, so I replaced "Geometry" with the newest
version, and that fixed that. I had to fix a bug where it was using the
"isnan" function as if it was in Math (i.e. Math::isNan), but I think
that must have been deprecated at some point; changed to read "isnan"
because that's now part of C++ standard lib.
And now I've got this new, exciting, bizzarre bug I don't have the
heart to solve, where it says this of compiling "EnergyRenderer.cpp":
g++ -c -o EnergyRenderer.o -D__LINUX__ -D__LITTLE_ENDIAN=1234
-D__BIG_ENDIAN=4321 -DFLTK_NEW -DFLTK_DOUBLE -DGL_GLEXT_PROTOTYPES
-ffriend-injection -I. -g0 -O3 -DNDEBUG -I/usr/include
EnergyRenderer.cpp In file included from EnergyRenderer.cpp:33:0:
ColorFunction.h:70:27: error: expected ‘;’ at end of member declaration
ColorFunction.h:70:37: error: expected ‘)’ before ‘number’
ColorFunction.h:86:27: error: expected ‘;’ at end of member declaration
ColorFunction.h:86:40: error: expected ‘)’ before ‘number’
EnergyRenderer.cpp: In member function ‘AtomClassifier*
EnergyRenderer::getClassifier()’: EnergyRenderer.cpp:639:61: error:
‘ColorFunction::get’ cannot be used as a function
make: *** [EnergyRenderer.o] Error 1
..I don't even know where to start with this crap. I don't code in C++,
I'm barely able to read it! :)
So, with my condolences, you've picked the most troublesome piece of
software I've seen in ages as your first use-case for Linux, which is
sad. I was sort of hoping this would be a case of "it's easy, just pop
up the software center and click install", as things usually are for
Linux these days.. :P
I'm attaching the modified source code I have so far that includes the
functioning version of Geometry and the "isnan" changes, if anyone else
who knows more about C++ wants to have a go at getting this to compile..
Best,
Cathal
Below is my original mail outlining the progress I made before losing
heart. It refers to "attached", but here's a link instead to the
archive, as I can't attach it through google groups:
https://anonfiles.com/file/a4c961f31541d7f38575c534ff20a5d1
(Yes, a zip rather than tar.gz, because bizarrely anonfiles.com doesn't
like gzip?)
--- Original Message ---
Hey John!
Welcome to Linux! Sorry you're having trouble already, but looking at
Protein Shop, that's not surprising. I tried to come up with a
comprehensive guide to getting it running, considering that the
developers don't offer compiled programs but rather only the source
code. Worse, it's got big dependencies; OpenGL and FLTK, plus others.
That'd be ok if it was pre-built, because you could just install OpenGL
and FLTK afterwards, but you need to install the "dev" versions of
those, and then build this.
So I tried. I installed all the dependencies and wrote a big email
explaining how, then downloaded the source code, uncompressed it, and
tried to build. Then I found that the source code bundles "Geometry"
and it doesn't compile, so I replaced "Geometry" with the newest
version, and that fixed that. I had to fix a bug where it was using the
"isnan" function as if it was in Math (i.e. Math::isNan), but I think
that must have been deprecated at some point; changed to read "isnan"
because that's now part of C++ standard lib.
And now I've got this new, exciting, bizzarre bug I don't have the
heart to solve, where it says this of compiling "EnergyRenderer.cpp":
g++ -c -o EnergyRenderer.o -D__LINUX__ -D__LITTLE_ENDIAN=1234
-D__BIG_ENDIAN=4321 -DFLTK_NEW -DFLTK_DOUBLE -DGL_GLEXT_PROTOTYPES
-ffriend-injection -I. -g0 -O3 -DNDEBUG -I/usr/include
EnergyRenderer.cpp In file included from EnergyRenderer.cpp:33:0:
ColorFunction.h:70:27: error: expected ‘;’ at end of member declaration
ColorFunction.h:70:37: error: expected ‘)’ before ‘number’
ColorFunction.h:86:27: error: expected ‘;’ at end of member declaration
ColorFunction.h:86:40: error: expected ‘)’ before ‘number’
EnergyRenderer.cpp: In member function ‘AtomClassifier*
EnergyRenderer::getClassifier()’: EnergyRenderer.cpp:639:61: error:
‘ColorFunction::get’ cannot be used as a function
make: *** [EnergyRenderer.o] Error 1
..I don't even know where to start with this crap. I don't code in C++,
I'm barely able to read it! :)
So, with my condolences, you've picked the most troublesome piece of
software I've seen in ages as your first use-case for Linux, which is
sad. I was sort of hoping this would be a case of "it's easy, just pop
up the software center and click install", as things usually are for
Linux these days.. :P
I'm attaching the modified source code I have so far that includes the
functioning version of Geometry and the "isnan" changes, if anyone else
who knows more about C++ wants to have a go at getting this to compile..
Best,
Cathal
Nathan McCorkle
Sep 19, 2013, 7:09:39 PM9/19/13
to diybio
I'm working on this too, will try updating Geometry, where did you get
it? I didn't find it in apt-cache search....
If you're running a 64-bit system, you could try downloading the RPM
file and using alien to convert it.... I'm not running 64-bit so I
can't confirm it will work:
wget sourcefourge.com/path/to/download
sudo apt-get install alien
sudo alien downloadedFile
it warned that I might need to invoke alien with the --script (or was
it scripts) option
--
-Nathan
it? I didn't find it in apt-cache search....
If you're running a 64-bit system, you could try downloading the RPM
file and using alien to convert it.... I'm not running 64-bit so I
can't confirm it will work:
wget sourcefourge.com/path/to/download
sudo apt-get install alien
sudo alien downloadedFile
it warned that I might need to invoke alien with the --script (or was
it scripts) option
-Nathan
William Heath
Sep 19, 2013, 7:35:24 PM9/19/13
to diy...@googlegroups.com
Hi All,
Can anyone interested in helping me to understand compilation issues on linux join me in #diybio on irc.freenode.net. My current error is:
centos@143 src]$ make
g++ -c -o TCPSocket2.o -D__LINUX__ -D__LITTLE_ENDIAN=1234 -D__BIG_ENDIAN=4321 -DFLTK_NEW -DFLTK_DOUBLE -DGL_GLEXT_PROTOTYPES -ffriend-injection -I. -g0 -O3 -DNDEBUG -I/usr/local/include TCPSocket2.cpp
In file included from ./Geometry/Box.h:28,
from Globals.h:41,
from TCPSocket2.cpp:27:
./Geometry/Point.h:46: error: declaration of ‘typedef class Geometry::Vector<ScalarParam, dimensionParam> Geometry::Point<ScalarParam, dimensionParam>::Vector’
./Geometry/Vector.h:33: error: changes meaning of ‘Vector’ from ‘class Geometry::Vector<ScalarParam, dimensionParam>’
./Geometry/Point.h:47: error: declaration of ‘typedef struct Geometry::AffineCombiner<ScalarParam, dimensionParam> Geometry::Point<ScalarParam, dimensionParam>::AffineCombiner’
./Geometry/Point.h:34: error: changes meaning of ‘AffineCombiner’ from ‘struct Geometry::AffineCombiner<ScalarParam, dimensionParam>’
In file included from ./Geometry/Box.h:30,
from Globals.h:41,
from TCPSocket2.cpp:27:
./Geometry/Ray.h:38: error: declaration of ‘typedef class Geometry::Vector<ScalarParam, dimensionParam> Geometry::Ray<ScalarParam, dimensionParam>::Vector’
./Geometry/Vector.h:33: error: changes meaning of ‘Vector’ from ‘class Geometry::Vector<ScalarParam, dimensionParam>’
./Geometry/Ray.h:39: error: declaration of ‘typedef class Geometry::Point<ScalarParam, dimensionParam> Geometry::Ray<ScalarParam, dimensionParam>::Point’
./Geometry/Point.h:38: error: changes meaning of ‘Point’ from ‘class Geometry::Point<ScalarParam, dimensionParam>’
In file included from Globals.h:41,
from TCPSocket2.cpp:27:
./Geometry/Box.h:54: error: declaration of ‘typedef class Geometry::Point<ScalarParam, dimensionParam> Geometry::Box<ScalarParam, dimensionParam>::Point’
./Geometry/Point.h:38: error: changes meaning of ‘Point’ from ‘class Geometry::Point<ScalarParam, dimensionParam>’
./Geometry/Box.h:55: error: declaration of ‘typedef class Geometry::Vector<ScalarParam, dimensionParam> Geometry::Box<ScalarParam, dimensionParam>::Vector’
./Geometry/Vector.h:33: error: changes meaning of ‘Vector’ from ‘class Geometry::Vector<ScalarParam, dimensionParam>’
./Geometry/Box.h:57: error: declaration of ‘typedef class Geometry::Ray<ScalarParam, dimensionParam> Geometry::Box<ScalarParam, dimensionParam>::Ray’
./Geometry/Ray.h:33: error: changes meaning of ‘Ray’ from ‘class Geometry::Ray<ScalarParam, dimensionParam>’
In file included from ./Geometry/OrthonormalTransformation.h:29,
from DragBox.h:22,
from Globals.h:43,
from TCPSocket2.cpp:27:
./Geometry/HVector.h:44: error: declaration of ‘typedef class Geometry::Vector<ScalarParam, dimensionParam> Geometry::HVector<ScalarParam, dimensionParam>::Vector’
./Geometry/Vector.h:33: error: changes meaning of ‘Vector’ from ‘class Geometry::Vector<ScalarParam, dimensionParam>’
./Geometry/HVector.h:45: error: declaration of ‘typedef class Geometry::Point<ScalarParam, dimensionParam> Geometry::HVector<ScalarParam, dimensionParam>::Point’
./Geometry/Point.h:38: error: changes meaning of ‘Point’ from ‘class Geometry::Point<ScalarParam, dimensionParam>’
In file included from ./Geometry/OrthonormalTransformation.h:30,
from DragBox.h:22,
from Globals.h:43,
from TCPSocket2.cpp:27:
./Geometry/Rotation.h:44: error: declaration of ‘typedef class Geometry::Vector<ScalarParam, dimensionParam> Geometry::Rotation<ScalarParam, dimensionParam>::Vector’
./Geometry/Vector.h:33: error: changes meaning of ‘Vector’ from ‘class Geometry::Vector<ScalarParam, dimensionParam>’
./Geometry/Rotation.h:45: error: declaration of ‘typedef class Geometry::Point<ScalarParam, dimensionParam> Geometry::Rotation<ScalarParam, dimensionParam>::Point’
./Geometry/Point.h:38: error: changes meaning of ‘Point’ from ‘class Geometry::Point<ScalarParam, dimensionParam>’
./Geometry/Rotation.h:46: error: declaration of ‘typedef class Geometry::HVector<ScalarParam, dimensionParam> Geometry::Rotation<ScalarParam, dimensionParam>::HVector’
./Geometry/HVector.h:35: error: changes meaning of ‘HVector’ from ‘class Geometry::HVector<ScalarParam, dimensionParam>’
./Geometry/Rotation.h:74: error: declaration of ‘typedef class Geometry::Vector<ScalarParam, 2> Geometry::Rotation<ScalarParam, 2>::Vector’
./Geometry/Vector.h:33: error: changes meaning of ‘Vector’ from ‘class Geometry::Vector<ScalarParam, 2>’
./Geometry/Rotation.h:75: error: declaration of ‘typedef class Geometry::Point<ScalarParam, 2> Geometry::Rotation<ScalarParam, 2>::Point’
./Geometry/Point.h:38: error: changes meaning of ‘Point’ from ‘class Geometry::Point<ScalarParam, 2>’
./Geometry/Rotation.h:76: error: declaration of ‘typedef class Geometry::HVector<ScalarParam, 2> Geometry::Rotation<ScalarParam, 2>::HVector’
./Geometry/HVector.h:35: error: changes meaning of ‘HVector’ from ‘class Geometry::HVector<ScalarParam, 2>’
./Geometry/Rotation.h:257: error: declaration of ‘typedef class Geometry::Vector<ScalarParam, 3> Geometry::Rotation<ScalarParam, 3>::Vector’
./Geometry/Vector.h:33: error: changes meaning of ‘Vector’ from ‘class Geometry::Vector<ScalarParam, 3>’
./Geometry/Rotation.h:258: error: declaration of ‘typedef class Geometry::Point<ScalarParam, 3> Geometry::Rotation<ScalarParam, 3>::Point’
./Geometry/Point.h:38: error: changes meaning of ‘Point’ from ‘class Geometry::Point<ScalarParam, 3>’
./Geometry/Rotation.h:259: error: declaration of ‘typedef class Geometry::HVector<ScalarParam, 3> Geometry::Rotation<ScalarParam, 3>::HVector’
./Geometry/HVector.h:35: error: changes meaning of ‘HVector’ from ‘class Geometry::HVector<ScalarParam, 3>’
In file included from DragBox.h:22,
from Globals.h:43,
from TCPSocket2.cpp:27:
./Geometry/OrthonormalTransformation.h:56: error: declaration of ‘typedef class Geometry::Vector<ScalarParam, dimensionParam> Geometry::OrthonormalTransformation<ScalarParam, dimensionParam>::Vector’
./Geometry/Vector.h:33: error: changes meaning of ‘Vector’ from ‘class Geometry::Vector<ScalarParam, dimensionParam>’
./Geometry/OrthonormalTransformation.h:57: error: declaration of ‘typedef class Geometry::Point<ScalarParam, dimensionParam> Geometry::OrthonormalTransformation<ScalarParam, dimensionParam>::Point’
./Geometry/Point.h:38: error: changes meaning of ‘Point’ from ‘class Geometry::Point<ScalarParam, dimensionParam>’
./Geometry/OrthonormalTransformation.h:58: error: declaration of ‘typedef class Geometry::HVector<ScalarParam, dimensionParam> Geometry::OrthonormalTransformation<ScalarParam, dimensionParam>::HVector’
./Geometry/HVector.h:35: error: changes meaning of ‘HVector’ from ‘class Geometry::HVector<ScalarParam, dimensionParam>’
./Geometry/OrthonormalTransformation.h:59: error: declaration of ‘typedef class Geometry::Rotation<ScalarParam, dimensionParam> Geometry::OrthonormalTransformation<ScalarParam, dimensionParam>::Rotation’
./Geometry/Rotation.h:39: error: changes meaning of ‘Rotation’ from ‘class Geometry::Rotation<ScalarParam, dimensionParam>’
In file included from DragBox.h:23,
from Globals.h:43,
from TCPSocket2.cpp:27:
./Geometry/ProjectiveTransformation.h:260: error: declaration of ‘typedef class Geometry::Vector<ScalarParam, dimensionParam> Geometry::ProjectiveTransformation<ScalarParam, dimensionParam>::Vector’
./Geometry/Vector.h:33: error: changes meaning of ‘Vector’ from ‘class Geometry::Vector<ScalarParam, dimensionParam>’
./Geometry/ProjectiveTransformation.h:261: error: declaration of ‘typedef class Geometry::Point<ScalarParam, dimensionParam> Geometry::ProjectiveTransformation<ScalarParam, dimensionParam>::Point’
./Geometry/Point.h:38: error: changes meaning of ‘Point’ from ‘class Geometry::Point<ScalarParam, dimensionParam>’
./Geometry/ProjectiveTransformation.h:262: error: declaration of ‘typedef class Geometry::HVector<ScalarParam, dimensionParam> Geometry::ProjectiveTransformation<ScalarParam, dimensionParam>::HVector’
./Geometry/HVector.h:35: error: changes meaning of ‘HVector’ from ‘class Geometry::HVector<ScalarParam, dimensionParam>’
./Geometry/ProjectiveTransformation.h:263: error: declaration of ‘typedef class Geometry::Rotation<ScalarParam, dimensionParam> Geometry::ProjectiveTransformation<ScalarParam, dimensionParam>::Rotation’
./Geometry/Rotation.h:39: error: changes meaning of ‘Rotation’ from ‘class Geometry::Rotation<ScalarParam, dimensionParam>’
./Geometry/ProjectiveTransformation.h:265: error: declaration of ‘typedef class Geometry::Matrix<ScalarParam, (dimensionParam + 1), (dimensionParam + 1)> Geometry::ProjectiveTransformation<ScalarParam, dimensionParam>::Matrix’
./Geometry/Matrix.h:196: error: changes meaning of ‘Matrix’ from ‘class Geometry::Matrix<ScalarParam, (dimensionParam + 1), (dimensionParam + 1)>’
In file included from ./Geometry/Sphere.h:30,
from Atom.h:22,
from Protein.h:28,
from Globals.h:44,
from TCPSocket2.cpp:27:
./Geometry/OrthogonalTransformation.h:59: error: declaration of ‘typedef class Geometry::Vector<ScalarParam, dimensionParam> Geometry::OrthogonalTransformation<ScalarParam, dimensionParam>::Vector’
./Geometry/Vector.h:33: error: changes meaning of ‘Vector’ from ‘class Geometry::Vector<ScalarParam, dimensionParam>’
./Geometry/OrthogonalTransformation.h:60: error: declaration of ‘typedef class Geometry::Point<ScalarParam, dimensionParam> Geometry::OrthogonalTransformation<ScalarParam, dimensionParam>::Point’
./Geometry/Point.h:38: error: changes meaning of ‘Point’ from ‘class Geometry::Point<ScalarParam, dimensionParam>’
./Geometry/OrthogonalTransformation.h:61: error: declaration of ‘typedef class Geometry::HVector<ScalarParam, dimensionParam> Geometry::OrthogonalTransformation<ScalarParam, dimensionParam>::HVector’
./Geometry/HVector.h:35: error: changes meaning of ‘HVector’ from ‘class Geometry::HVector<ScalarParam, dimensionParam>’
./Geometry/OrthogonalTransformation.h:62: error: declaration of ‘typedef class Geometry::Rotation<ScalarParam, dimensionParam> Geometry::OrthogonalTransformation<ScalarParam, dimensionParam>::Rotation’
./Geometry/Rotation.h:39: error: changes meaning of ‘Rotation’ from ‘class Geometry::Rotation<ScalarParam, dimensionParam>’
In file included from Atom.h:22,
from Protein.h:28,
from Globals.h:44,
from TCPSocket2.cpp:27:
./Geometry/Sphere.h:43: error: declaration of ‘typedef class Geometry::Vector<ScalarParam, dimensionParam> Geometry::Sphere<ScalarParam, dimensionParam>::Vector’
./Geometry/Vector.h:33: error: changes meaning of ‘Vector’ from ‘class Geometry::Vector<ScalarParam, dimensionParam>’
./Geometry/Sphere.h:44: error: declaration of ‘typedef class Geometry::Point<ScalarParam, dimensionParam> Geometry::Sphere<ScalarParam, dimensionParam>::Point’
./Geometry/Point.h:38: error: changes meaning of ‘Point’ from ‘class Geometry::Point<ScalarParam, dimensionParam>’
./Geometry/Sphere.h:45: error: declaration of ‘typedef class Geometry::Ray<ScalarParam, dimensionParam> Geometry::Sphere<ScalarParam, dimensionParam>::Ray’
./Geometry/Ray.h:33: error: changes meaning of ‘Ray’ from ‘class Geometry::Ray<ScalarParam, dimensionParam>’
In file included from ProteinRenderer.h:30,
from ProteinInteractor.h:43,
from Globals.h:46,
from TCPSocket2.cpp:27:
./Geometry/SplineCurve.h:53: error: declaration of ‘typedef class Geometry::Vector<ScalarParam, dimensionParam> Geometry::SplineCurve<ScalarParam, dimensionParam>::Vector’
./Geometry/Vector.h:33: error: changes meaning of ‘Vector’ from ‘class Geometry::Vector<ScalarParam, dimensionParam>’
./Geometry/SplineCurve.h:54: error: declaration of ‘typedef class Geometry::Point<ScalarParam, dimensionParam> Geometry::SplineCurve<ScalarParam, dimensionParam>::Point’
./Geometry/Point.h:38: error: changes meaning of ‘Point’ from ‘class Geometry::Point<ScalarParam, dimensionParam>’
In file included from IK.h:24,
from ProteinInteractor.h:45,
from Globals.h:46,
from TCPSocket2.cpp:27:
./Geometry/AffineTransformation.h:167: error: declaration of ‘typedef class Geometry::Vector<ScalarParam, dimensionParam> Geometry::AffineTransformation<ScalarParam, dimensionParam>::Vector’
./Geometry/Vector.h:33: error: changes meaning of ‘Vector’ from ‘class Geometry::Vector<ScalarParam, dimensionParam>’
./Geometry/AffineTransformation.h:168: error: declaration of ‘typedef class Geometry::Point<ScalarParam, dimensionParam> Geometry::AffineTransformation<ScalarParam, dimensionParam>::Point’
./Geometry/Point.h:38: error: changes meaning of ‘Point’ from ‘class Geometry::Point<ScalarParam, dimensionParam>’
./Geometry/AffineTransformation.h:169: error: declaration of ‘typedef class Geometry::HVector<ScalarParam, dimensionParam> Geometry::AffineTransformation<ScalarParam, dimensionParam>::HVector’
./Geometry/HVector.h:35: error: changes meaning of ‘HVector’ from ‘class Geometry::HVector<ScalarParam, dimensionParam>’
./Geometry/AffineTransformation.h:170: error: declaration of ‘typedef class Geometry::Rotation<ScalarParam, dimensionParam> Geometry::AffineTransformation<ScalarParam, dimensionParam>::Rotation’
./Geometry/Rotation.h:39: error: changes meaning of ‘Rotation’ from ‘class Geometry::Rotation<ScalarParam, dimensionParam>’
./Geometry/AffineTransformation.h:172: error: declaration of ‘typedef class Geometry::Matrix<ScalarParam, dimensionParam, (dimensionParam + 1)> Geometry::AffineTransformation<ScalarParam, dimensionParam>::Matrix’
./Geometry/Matrix.h:196: error: changes meaning of ‘Matrix’ from ‘class Geometry::Matrix<ScalarParam, dimensionParam, (dimensionParam + 1)>’
make: *** [TCPSocket2.o] Error 1
-Tim
To view this discussion on the web visit https://groups.google.com/d/msgid/diybio/CA%2B82U9%2B-RJTBCMMs-KhXbv-oiGLBSw6Ouh6Hma8pUE1r-GyWCg%40mail.gmail.com.
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Cathal Garvey
Sep 19, 2013, 8:03:03 PM9/19/13
to diy...@googlegroups.com
Hi Tim,
Those errors are what I got prior to replacing the Geometry toolkit
with a more up-to-date version. That's the biggest change in the zipped
codebase I linked to in my prior mail.
On Thu, 19 Sep 2013 13:35:24 -1000
> 2>‘Vector’ from ‘class
> dimensionParam>meaning of ‘Matrix’ from ‘class
Those errors are what I got prior to replacing the Geometry toolkit
with a more up-to-date version. That's the biggest change in the zipped
codebase I linked to in my prior mail.
On Thu, 19 Sep 2013 13:35:24 -1000
> Geometry::Vector<ScalarParam, 2>’
> ./Geometry/Rotation.h:75: error: declaration of ‘typedef class
> Geometry::Point<ScalarParam, 2> Geometry::Rotation<ScalarParam,
> 2>::Point’ ./Geometry/Point.h:38: error: changes meaning of ‘Point’
> 2>from ‘class
> ./Geometry/Rotation.h:75: error: declaration of ‘typedef class
> Geometry::Point<ScalarParam, 2> Geometry::Rotation<ScalarParam,
> 2>::Point’ ./Geometry/Point.h:38: error: changes meaning of ‘Point’
> Geometry::Point<ScalarParam, 2>’
> ./Geometry/Rotation.h:76: error: declaration of ‘typedef class
> Geometry::HVector<ScalarParam, 2> Geometry::Rotation<ScalarParam,
> 2>::HVector’
> ./Geometry/HVector.h:35: error: changes meaning of ‘HVector’ from
> ‘class Geometry::HVector<ScalarParam, 2>’
> ./Geometry/Rotation.h:257: error: declaration of ‘typedef class
> Geometry::Vector<ScalarParam, 3> Geometry::Rotation<ScalarParam,
> 3>::Vector’ ./Geometry/Vector.h:33: error: changes meaning of
> 3>‘Vector’ from ‘class
> ./Geometry/Rotation.h:76: error: declaration of ‘typedef class
> Geometry::HVector<ScalarParam, 2> Geometry::Rotation<ScalarParam,
> 2>::HVector’
> ./Geometry/HVector.h:35: error: changes meaning of ‘HVector’ from
> ‘class Geometry::HVector<ScalarParam, 2>’
> ./Geometry/Rotation.h:257: error: declaration of ‘typedef class
> Geometry::Vector<ScalarParam, 3> Geometry::Rotation<ScalarParam,
> 3>::Vector’ ./Geometry/Vector.h:33: error: changes meaning of
> Geometry::Vector<ScalarParam, 3>’
> ./Geometry/Rotation.h:258: error: declaration of ‘typedef class
> Geometry::Point<ScalarParam, 3> Geometry::Rotation<ScalarParam,
> 3>::Point’ ./Geometry/Point.h:38: error: changes meaning of ‘Point’
> 3>from ‘class
> ./Geometry/Rotation.h:258: error: declaration of ‘typedef class
> Geometry::Point<ScalarParam, 3> Geometry::Rotation<ScalarParam,
> 3>::Point’ ./Geometry/Point.h:38: error: changes meaning of ‘Point’
> Geometry::Point<ScalarParam, 3>’
> ./Geometry/Rotation.h:259: error: declaration of ‘typedef class
> Geometry::HVector<ScalarParam, 3> Geometry::Rotation<ScalarParam,
> 3>::HVector’
> ./Geometry/HVector.h:35: error: changes meaning of ‘HVector’ from
> ‘class Geometry::HVector<ScalarParam, 3>’
> In file included from DragBox.h:22,
> from Globals.h:43,
> from TCPSocket2.cpp:27:
> ./Geometry/OrthonormalTransformation.h:56: error: declaration of
> ‘typedef class Geometry::Vector<ScalarParam, dimensionParam>
> Geometry::OrthonormalTransformation<ScalarParam,
> dimensionParam>::Vector’ ./Geometry/Vector.h:33: error: changes
> dimensionParam>meaning of ‘Vector’ from ‘class
> ./Geometry/Rotation.h:259: error: declaration of ‘typedef class
> Geometry::HVector<ScalarParam, 3> Geometry::Rotation<ScalarParam,
> 3>::HVector’
> ./Geometry/HVector.h:35: error: changes meaning of ‘HVector’ from
> ‘class Geometry::HVector<ScalarParam, 3>’
> In file included from DragBox.h:22,
> from Globals.h:43,
> from TCPSocket2.cpp:27:
> ./Geometry/OrthonormalTransformation.h:56: error: declaration of
> ‘typedef class Geometry::Vector<ScalarParam, dimensionParam>
> Geometry::OrthonormalTransformation<ScalarParam,
> dimensionParam>::Vector’ ./Geometry/Vector.h:33: error: changes
> Geometry::Vector<ScalarParam, dimensionParam>’
> ./Geometry/OrthonormalTransformation.h:57: error: declaration of
> ‘typedef class Geometry::Point<ScalarParam, dimensionParam>
> Geometry::OrthonormalTransformation<ScalarParam,
> dimensionParam>::Point’ ./Geometry/Point.h:38: error: changes meaning
> dimensionParam>of ‘Point’ from ‘class
> ./Geometry/OrthonormalTransformation.h:57: error: declaration of
> ‘typedef class Geometry::Point<ScalarParam, dimensionParam>
> Geometry::OrthonormalTransformation<ScalarParam,
> dimensionParam>::Point’ ./Geometry/Point.h:38: error: changes meaning
> Geometry::Point<ScalarParam, dimensionParam>’
> ./Geometry/OrthonormalTransformation.h:58: error: declaration of
> ‘typedef class Geometry::HVector<ScalarParam, dimensionParam>
> Geometry::OrthonormalTransformation<ScalarParam,
> dimensionParam>::HVector’ ./Geometry/HVector.h:35: error: changes
> dimensionParam>meaning of ‘HVector’ from ‘class
> ./Geometry/OrthonormalTransformation.h:58: error: declaration of
> ‘typedef class Geometry::HVector<ScalarParam, dimensionParam>
> Geometry::OrthonormalTransformation<ScalarParam,
> dimensionParam>::HVector’ ./Geometry/HVector.h:35: error: changes
> Geometry::HVector<ScalarParam, dimensionParam>’
> ./Geometry/OrthonormalTransformation.h:59: error: declaration of
> ‘typedef class Geometry::Rotation<ScalarParam, dimensionParam>
> Geometry::OrthonormalTransformation<ScalarParam,
> dimensionParam>::Rotation’ ./Geometry/Rotation.h:39: error: changes
> dimensionParam>meaning of ‘Rotation’ from ‘class
> ./Geometry/OrthonormalTransformation.h:59: error: declaration of
> ‘typedef class Geometry::Rotation<ScalarParam, dimensionParam>
> Geometry::OrthonormalTransformation<ScalarParam,
> dimensionParam>::Rotation’ ./Geometry/Rotation.h:39: error: changes
> Geometry::Rotation<ScalarParam, dimensionParam>’
> In file included from DragBox.h:23,
> from Globals.h:43,
> from TCPSocket2.cpp:27:
> ./Geometry/ProjectiveTransformation.h:260: error: declaration of
> ‘typedef class Geometry::Vector<ScalarParam, dimensionParam>
> Geometry::ProjectiveTransformation<ScalarParam,
> dimensionParam>::Vector’ ./Geometry/Vector.h:33: error: changes
> dimensionParam>meaning of ‘Vector’ from ‘class
> In file included from DragBox.h:23,
> from Globals.h:43,
> from TCPSocket2.cpp:27:
> ./Geometry/ProjectiveTransformation.h:260: error: declaration of
> ‘typedef class Geometry::Vector<ScalarParam, dimensionParam>
> Geometry::ProjectiveTransformation<ScalarParam,
> dimensionParam>::Vector’ ./Geometry/Vector.h:33: error: changes
> Geometry::Vector<ScalarParam, dimensionParam>’
> ./Geometry/ProjectiveTransformation.h:261: error: declaration of
> ‘typedef class Geometry::Point<ScalarParam, dimensionParam>
> Geometry::ProjectiveTransformation<ScalarParam,
> dimensionParam>::Point’ ./Geometry/Point.h:38: error: changes meaning
> dimensionParam>of ‘Point’ from ‘class
> ./Geometry/ProjectiveTransformation.h:261: error: declaration of
> ‘typedef class Geometry::Point<ScalarParam, dimensionParam>
> Geometry::ProjectiveTransformation<ScalarParam,
> dimensionParam>::Point’ ./Geometry/Point.h:38: error: changes meaning
> Geometry::Point<ScalarParam, dimensionParam>’
> ./Geometry/ProjectiveTransformation.h:262: error: declaration of
> ‘typedef class Geometry::HVector<ScalarParam, dimensionParam>
> Geometry::ProjectiveTransformation<ScalarParam,
> dimensionParam>::HVector’ ./Geometry/HVector.h:35: error: changes
> dimensionParam>meaning of ‘HVector’ from ‘class
> ./Geometry/ProjectiveTransformation.h:262: error: declaration of
> ‘typedef class Geometry::HVector<ScalarParam, dimensionParam>
> Geometry::ProjectiveTransformation<ScalarParam,
> dimensionParam>::HVector’ ./Geometry/HVector.h:35: error: changes
> Geometry::HVector<ScalarParam, dimensionParam>’
> ./Geometry/ProjectiveTransformation.h:263: error: declaration of
> ‘typedef class Geometry::Rotation<ScalarParam, dimensionParam>
> Geometry::ProjectiveTransformation<ScalarParam,
> dimensionParam>::Rotation’ ./Geometry/Rotation.h:39: error: changes
> dimensionParam>meaning of ‘Rotation’ from ‘class
> ./Geometry/ProjectiveTransformation.h:263: error: declaration of
> ‘typedef class Geometry::Rotation<ScalarParam, dimensionParam>
> Geometry::ProjectiveTransformation<ScalarParam,
> dimensionParam>::Rotation’ ./Geometry/Rotation.h:39: error: changes
> Geometry::Rotation<ScalarParam, dimensionParam>’
> ./Geometry/ProjectiveTransformation.h:265: error: declaration of
> ‘typedef class Geometry::Matrix<ScalarParam, (dimensionParam + 1),
> (dimensionParam + 1)> Geometry::ProjectiveTransformation<ScalarParam,
> dimensionParam>::Matrix’ ./Geometry/Matrix.h:196: error: changes
> dimensionParam>meaning of ‘Matrix’ from ‘class
> ./Geometry/ProjectiveTransformation.h:265: error: declaration of
> ‘typedef class Geometry::Matrix<ScalarParam, (dimensionParam + 1),
> (dimensionParam + 1)> Geometry::ProjectiveTransformation<ScalarParam,
> dimensionParam>::Matrix’ ./Geometry/Matrix.h:196: error: changes
> Geometry::Matrix<ScalarParam, (dimensionParam + 1), (dimensionParam +
> 1)>’ In file included from ./Geometry/Sphere.h:30,
> from Atom.h:22,
> from Protein.h:28,
> from Globals.h:44,
> from TCPSocket2.cpp:27:
> ./Geometry/OrthogonalTransformation.h:59: error: declaration of
> ‘typedef class Geometry::Vector<ScalarParam, dimensionParam>
> Geometry::OrthogonalTransformation<ScalarParam,
> dimensionParam>::Vector’ ./Geometry/Vector.h:33: error: changes
> dimensionParam>meaning of ‘Vector’ from ‘class
> 1)>’ In file included from ./Geometry/Sphere.h:30,
> from Atom.h:22,
> from Protein.h:28,
> from Globals.h:44,
> from TCPSocket2.cpp:27:
> ./Geometry/OrthogonalTransformation.h:59: error: declaration of
> ‘typedef class Geometry::Vector<ScalarParam, dimensionParam>
> Geometry::OrthogonalTransformation<ScalarParam,
> dimensionParam>::Vector’ ./Geometry/Vector.h:33: error: changes
> Geometry::Vector<ScalarParam, dimensionParam>’
> ./Geometry/OrthogonalTransformation.h:60: error: declaration of
> ‘typedef class Geometry::Point<ScalarParam, dimensionParam>
> Geometry::OrthogonalTransformation<ScalarParam,
> dimensionParam>::Point’ ./Geometry/Point.h:38: error: changes meaning
> dimensionParam>of ‘Point’ from ‘class
> ./Geometry/OrthogonalTransformation.h:60: error: declaration of
> ‘typedef class Geometry::Point<ScalarParam, dimensionParam>
> Geometry::OrthogonalTransformation<ScalarParam,
> dimensionParam>::Point’ ./Geometry/Point.h:38: error: changes meaning
> Geometry::Point<ScalarParam, dimensionParam>’
> ./Geometry/OrthogonalTransformation.h:61: error: declaration of
> ‘typedef class Geometry::HVector<ScalarParam, dimensionParam>
> Geometry::OrthogonalTransformation<ScalarParam,
> dimensionParam>::HVector’ ./Geometry/HVector.h:35: error: changes
> dimensionParam>meaning of ‘HVector’ from ‘class
> ./Geometry/OrthogonalTransformation.h:61: error: declaration of
> ‘typedef class Geometry::HVector<ScalarParam, dimensionParam>
> Geometry::OrthogonalTransformation<ScalarParam,
> dimensionParam>::HVector’ ./Geometry/HVector.h:35: error: changes
> Geometry::HVector<ScalarParam, dimensionParam>’
> ./Geometry/OrthogonalTransformation.h:62: error: declaration of
> ‘typedef class Geometry::Rotation<ScalarParam, dimensionParam>
> Geometry::OrthogonalTransformation<ScalarParam,
> dimensionParam>::Rotation’ ./Geometry/Rotation.h:39: error: changes
> dimensionParam>meaning of ‘Rotation’ from ‘class
> ./Geometry/OrthogonalTransformation.h:62: error: declaration of
> ‘typedef class Geometry::Rotation<ScalarParam, dimensionParam>
> Geometry::OrthogonalTransformation<ScalarParam,
> dimensionParam>::Rotation’ ./Geometry/Rotation.h:39: error: changes
William Heath
Sep 19, 2013, 8:07:55 PM9/19/13
to diy...@googlegroups.com
Hi Cathal,
The problem with your last compilation error is uint is not defined, replace it with unsigned int. It will then get past that error!
-Tim
P.S.
static ColorFunction * get(unsigned int number);
static ColorFunction * remove(unsigned int number);
Cathal Garvey
Sep 19, 2013, 8:22:01 PM9/19/13
to diy...@googlegroups.com
> I'm working on this too, will try updating Geometry, where did you get
> it? I didn't find it in apt-cache search....
http://idav.ucdavis.edu/~okreylos/ResDev/Geometry/Download.html
> it? I didn't find it in apt-cache search....
Literally deleted the "Geometry" folder in the src directory and
replaced with the one from this archive.
Nathan McCorkle
Sep 19, 2013, 8:35:50 PM9/19/13
to diybio
Interestingly, I downloaded that anonfile zip, typed make without
messing with the Makefile and it gave me an error about fluid, not the
EnergyRenderer.... I installed libfltk1.1-dev so far, along with the
binary packages and the fltk gl binary package. Ahh, ok after
installing fluid (sudo apt-get install fluid) I got the EnergyRenderer
error and made the changes Heath pointed out in ColorFunction.h (uint
to unsigned int).
Then I had to change Globals.cpp line 75 from
char *ext = strrchr(basename, '.');
to:
char const *ext
Then in SpaceBall.h I had to change <string> to <string.h>
Now I'm getting an error that g77 isn't present, and it's not
apparently in the ubuntu repo.
-Nathan
messing with the Makefile and it gave me an error about fluid, not the
EnergyRenderer.... I installed libfltk1.1-dev so far, along with the
binary packages and the fltk gl binary package. Ahh, ok after
installing fluid (sudo apt-get install fluid) I got the EnergyRenderer
error and made the changes Heath pointed out in ColorFunction.h (uint
to unsigned int).
Then I had to change Globals.cpp line 75 from
char *ext = strrchr(basename, '.');
to:
char const *ext
Then in SpaceBall.h I had to change <string> to <string.h>
Now I'm getting an error that g77 isn't present, and it's not
apparently in the ubuntu repo.
-Nathan
William Heath
Sep 19, 2013, 8:43:33 PM9/19/13
to diy...@googlegroups.com
sudo yum install compat-gcc-34-g77.i686
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Nathan McCorkle
Sep 19, 2013, 8:54:58 PM9/19/13
to diybio
On Thu, Sep 19, 2013 at 5:43 PM, William Heath <wgh...@gmail.com> wrote:
> sudo yum install compat-gcc-34-g77.i686
hmm, says 'No package compat-gcc-34-g77.i686 available'
> sudo yum install compat-gcc-34-g77.i686
hmm, says 'No package compat-gcc-34-g77.i686 available'
Josiah Zayner
Sep 19, 2013, 9:19:31 PM9/19/13
to diy...@googlegroups.com
Yeah I found where to install g77 from http://askubuntu.com/questions/346278/really-need-g77-on-ubuntu-12-04-cant-install
Now a messed up error:
LLineIlluminator.o: In function `GLLineIlluminator::enableLighting(GLContextData&) const':
GLLineIlluminator.cpp:(.text+0x176a): undefined reference to `Geometry::ComponentArray<float, 3>::ComponentArray<float, 4>(Geometry::ComponentArray<float, 4> const&)'
GLLineIlluminator.cpp:(.text+0x17a2): undefined reference to `Geometry::ComponentArray<float, 3>::ComponentArray<float, 4>(Geometry::ComponentArray<float, 4> const&)'
collect2: ld returned 1 exit status
make: *** [ProteinShop] Error 1
I include GLGeometry.h in GLLineIlluminator.cpp tried changed the type of ComponentArray in GLGeometry.h from ScalarType to GLfloat. Some other stuff and still no luck.
I have tried a bunch of stuff no luck so far.
William Heath
Sep 19, 2013, 9:20:58 PM9/19/13
to diy...@googlegroups.com
Yes that is where I am stuck now as well.
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Josiah Zayner
Sep 19, 2013, 9:59:12 PM9/19/13
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The code appears broke beyond brokenness. The website is down http://proteinshop.lbl.gov/Index.html. I would try emaling Sylvia at SNCrivelli [at] lbl.gov if you really want to try and get it working. However.
If you want to do similar stuff I would install VMD http://www.ks.uiuc.edu/Research/vmd/
or pymol: sudo apt-get install pymol
for secondary structure prediction try PSIPRED: http://bioinf.cs.ucl.ac.uk/psipred/
And for protein structure prediction use: http://swissmodel.expasy.org/ if it has some homology to some other structure
or http://godzilla.uchicago.edu/cgi-bin/aashish2/TerItFix/TerItFix.cgi if it does not have any homology
for Molecular Dynamics Simulations try namd which comes with VMD or gromacs: sudo apt-get install gromacs
William Heath
Sep 19, 2013, 10:08:18 PM9/19/13
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Hi All,
I got it to compile! Here is a screenshot of it running:
Where can I get a pdb file or .pred file to test that it works?
-Tim
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Josiah Zayner
Sep 19, 2013, 10:10:47 PM9/19/13
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William Heath
Sep 19, 2013, 10:20:37 PM9/19/13
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Hi All,
It segfaulted reading the pdb. Here is the output:
Is there another simpler pdb it could read you think?
-Tim
P.S.
I just removed all code from void GLLineIlluminator::enableLighting(GLContextData& contextData) const to get it to compile. I will fix that later, just want to see what is possible.
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Josiah Zayner
Sep 19, 2013, 10:23:13 PM9/19/13
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ubiquitin probably the simplest structure you can find
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William Heath
Sep 19, 2013, 10:29:04 PM9/19/13
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Nathan McCorkle
Sep 19, 2013, 10:32:59 PM9/19/13
to diybio
On Thu, Sep 19, 2013 at 6:20 PM, William Heath <wgh...@gmail.com> wrote:
> Yes that is where I am stuck now as well.
>
>
> On Thu, Sep 19, 2013 at 3:19 PM, Josiah Zayner <josiah...@gmail.com>
> wrote:
>>
>> Yeah I found where to install g77 from
>> http://askubuntu.com/questions/346278/really-need-g77-on-ubuntu-12-04-cant-install
>>
>> Now a messed up error:
>> LLineIlluminator.o: In function
>> `GLLineIlluminator::enableLighting(GLContextData&) const':
>> GLLineIlluminator.cpp:(.text+0x176a): undefined reference to
>> `Geometry::ComponentArray<float, 3>::ComponentArray<float,
>> 4>(Geometry::ComponentArray<float, 4> const&)'
>> GLLineIlluminator.cpp:(.text+0x17a2): undefined reference to
>> `Geometry::ComponentArray<float, 3>::ComponentArray<float,
>> 4>(Geometry::ComponentArray<float, 4> const&)'
>> collect2: ld returned 1 exit status
>> make: *** [ProteinShop] Error 1
>>
Ok I got past this by adding
> Yes that is where I am stuck now as well.
>
>
> On Thu, Sep 19, 2013 at 3:19 PM, Josiah Zayner <josiah...@gmail.com>
> wrote:
>>
>> Yeah I found where to install g77 from
>> http://askubuntu.com/questions/346278/really-need-g77-on-ubuntu-12-04-cant-install
>>
>> Now a messed up error:
>> LLineIlluminator.o: In function
>> `GLLineIlluminator::enableLighting(GLContextData&) const':
>> GLLineIlluminator.cpp:(.text+0x176a): undefined reference to
>> `Geometry::ComponentArray<float, 3>::ComponentArray<float,
>> 4>(Geometry::ComponentArray<float, 4> const&)'
>> GLLineIlluminator.cpp:(.text+0x17a2): undefined reference to
>> `Geometry::ComponentArray<float, 3>::ComponentArray<float,
>> 4>(Geometry::ComponentArray<float, 4> const&)'
>> collect2: ld returned 1 exit status
>> make: *** [ProteinShop] Error 1
>>
template ComponentArray<float,3>::ComponentArray(const
ComponentArray<float,4>&);
after line 62 in src/Geometry/ComponentArray.cpp
but it just buffer overflows when I start it before loading anything
on the screen.
William Heath
Sep 19, 2013, 11:51:52 PM9/19/13
to diy...@googlegroups.com
Hi All,
I created a virtual box centos 6.4 x86 appliance with gnome and protein shop on it. You can download it here:
This is my first time doing a torrent, tell me if it works :>
-Tim
P.S.
You can also just download the file directly via http download.
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Josiah Zayner
Sep 20, 2013, 9:08:56 AM9/20/13
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I tried what you said (commenting out the GLLineIlluminator::enableLighting function) . It also buffer overflowed and core dumped like Nathan.
Can you post the actual code or a diff of the file you modified?
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Meredith L. Patterson
Sep 20, 2013, 12:16:49 PM9/20/13
to DIYBio Mailing List
Yeah Tim! Go team you!
Did you manage to figure out what happened with the pdb that segfaulted? It sounds like this might be an ongoing project. Are you familiar with travis-ci? If you've got the beginnings of a test suite together (ubiquitin, the one that segfaulted, ?), we could put the code into github and set up automated builds. I'd be happy to help with that.
Cheers,
--mlp
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Nathan McCorkle
Sep 20, 2013, 1:30:13 PM9/20/13
to diybio
On Fri, Sep 20, 2013 at 6:08 AM, Josiah Zayner <josiah...@gmail.com> wrote:
> I tried what you said (commenting out the GLLineIlluminator::enableLighting
> function) . It also buffer overflowed and core dumped like Nathan.
When did Tim say to do that? I don't see that message. I didn't
> I tried what you said (commenting out the GLLineIlluminator::enableLighting
> function) . It also buffer overflowed and core dumped like Nathan.
comment anything out to get it compiling!
Josiah Zayner
Sep 20, 2013, 2:22:10 PM9/20/13
to diy...@googlegroups.com
>-Tim
>P.S.
>I just removed all code from void GLLineIlluminator::enableLighting(GLContextData& contextData) const to get it to compile. I will fix that later, >just want to see what is possible.
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John Dohnal
Sep 20, 2013, 3:12:01 PM9/20/13
to diy...@googlegroups.com, cathal...@cathalgarvey.me
Lol, I think it may be a little of both! Thanks for trying to help me, I'm just sorry you put so much effort into trying to get it to work!
Best,
John
John Dohnal
Sep 20, 2013, 3:23:35 PM9/20/13
to diy...@googlegroups.com
Hey whg,
Wow, you people really know how to plow some hard soil! Didn't understand any of it, but GO TEAM DIYBIO!
If its as buggy as you all say it is, I may be better off going with the other software recommendations, but if y'all can get it to run, I'll be in your debt!
Thanks,
John
Wow, you people really know how to plow some hard soil! Didn't understand any of it, but GO TEAM DIYBIO!
If its as buggy as you all say it is, I may be better off going with the other software recommendations, but if y'all can get it to run, I'll be in your debt!
Thanks,
John
William Heath
Sep 20, 2013, 4:30:08 PM9/20/13
to diy...@googlegroups.com
Hi All,
I don't know why I am not making myself clear. I DID GET PROTEIN SHOP TO COMPILE AND WORK!!!! Please download the oracle virtual box appliance right here!!!
Go to www.graysonconsulting.biz to see the login info and other information you will need. Please stop making this harder than it is. When you boot up the oracle virtual box image it will go directly into protein shop loading ubiquitin!!! Can someone just do this once so I can feel sane and that someone somewhere understands what I did and why it is good pretty please?
-Tim
P.S.
Meredith I would like to put this in github any help doing that is appreciated. I don't know why it segfaulted on a different protein other than ubiquitin but it did. One of my major goals is 3d design with dna where the cell grows into a particular shape, with particular cells of my design. I know it involves hedgehog genes etc... Just like we give a model to a 3d printer, I want to give a model to a program and have it output the dna necessary to grow the 3d model. Any ideas on the best way to do that? I have been told there are gaps in biological embriology knowledge that doesn't make this feasible. My idea is to make assumptions and fill in the gaps as knowledge increases but at the same time discovering small experiments to try to test theories. My idea is to use the zebra fish (http://www.youtube.com/watch?v=wJNRIDWjX-o) for my growing platform as it has a transparent egg to watch things growing. I know protein cascade diffusion trigger cells to grow and change etc... My idea is to use differential equations of diffusion along with biobricks to sense proteins to cause the zebra fish egg to grow in the desired way. Let me know your ideas.
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Josiah Zayner
Sep 20, 2013, 4:37:53 PM9/20/13
to diy...@googlegroups.com
Tim we appreciate your help but it would be much easier if you just posted a diff of the code you changed so it doesn't require someone using a virtual box to run the program. And we can test if it works on different platforms. If you can just run the diff commands against the original and new GLLineIlluminator.cpp file that would be very helpful.
Thanks.
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Meredith L. Patterson
Sep 20, 2013, 5:37:39 PM9/20/13
to DIYBio Mailing List
Let's get it into github to start with. Tim, do you know how to do that? If not, mail me a tarball of your source offlist?
Cheers,
--mlp
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William Heath
Sep 20, 2013, 5:45:05 PM9/20/13
to diy...@googlegroups.com
Hi Meredith,
I am importing into github now.
-Tim
P.S.
The repository will be located here:
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William Heath
Sep 20, 2013, 6:07:39 PM9/20/13
to diy...@googlegroups.com
Hi All,
I have imported my protein shop source code that I got to compile on centos 6.4. Please feel free to check it out and compile it!
-Tim
P.S.
The location of the repository is at: https://github.com/wheath/protein-shop
Nathan McCorkle
Sep 20, 2013, 6:08:07 PM9/20/13
to diybio
On Thu, Sep 19, 2013 at 8:51 PM, William Heath <wgh...@gmail.com> wrote:
> Hi All,
>
> I created a virtual box centos 6.4 x86 appliance with gnome and protein shop
> on it. You can download it here:
>
> http://209.160.65.90/
William, I opened the .ova and it imported into VirtualBox, but upon
> Hi All,
>
> I created a virtual box centos 6.4 x86 appliance with gnome and protein shop
> on it. You can download it here:
>
> http://209.160.65.90/
logging in and even switching to root, I don't see ProteinShop on
there... your web page says it should be in /home/centos/work but
~/work doesn't exist
William Heath
Sep 20, 2013, 6:14:07 PM9/20/13
to diy...@googlegroups.com
Hi Nathan,
I am downloading it and checking it now.
-Tim
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Nathan McCorkle
Sep 20, 2013, 6:15:26 PM9/20/13
to diybio
So I changed the compile option flags to include debugging symbols,
and it's working now! I'm not sure what that changed since there were
two compile options I omitted, but here's a pic to prove it's running
in ubuntu:
http://imgur.com/oDnvPEH
I didn't delete any code like Tim and Josiah did.
I commented out the line
CFLAGS = -g0 -03 -DNDEBUG
and changed it to just
CFLAGS = -g
(in src/Makefile)
and it's working now! I'm not sure what that changed since there were
two compile options I omitted, but here's a pic to prove it's running
in ubuntu:
http://imgur.com/oDnvPEH
I didn't delete any code like Tim and Josiah did.
I commented out the line
CFLAGS = -g0 -03 -DNDEBUG
and changed it to just
CFLAGS = -g
(in src/Makefile)
Josiah Zayner
Sep 20, 2013, 6:27:04 PM9/20/13
to diy...@googlegroups.com
Neither methods work for me. Oh well. Still buffer overflows and core dumps. Looks like a libc issue. What version you all running?
$uname -a
Linux Ono-Sendai 3.5.0-18-generic #29-Ubuntu SMP Thu Oct 25 07:26:14 UTC 2012 x86_64 x86_64 x86_64 GNU/Linux
case@Ono-Sendai:~/Downloads/ProteinShop/bin$ ./ProteinShop
*** buffer overflow detected ***: ./ProteinShop terminated
======= Backtrace: =========
/lib/x86_64-linux-gnu/libc.so.6(__fortify_fail+0x37)[0x7f603117a817]
/lib/x86_64-linux-gnu/libc.so.6(+0x109710)[0x7f6031179710]
/lib/x86_64-linux-gnu/libc.so.6(+0x108b79)[0x7f6031178b79]
/lib/x86_64-linux-gnu/libc.so.6(_IO_default_xsputn+0xdd)[0x7f60310ec13d]
/lib/x86_64-linux-gnu/libc.so.6(_IO_vfprintf+0x1d42)[0x7f60310ba702]
/lib/x86_64-linux-gnu/libc.so.6(__vsprintf_chk+0x94)[0x7f6031178c14]
/lib/x86_64-linux-gnu/libc.so.6(__sprintf_chk+0x7d)[0x7f6031178b5d]
./ProteinShop[0x516378]
./ProteinShop(main+0x60)[0x4648a0]
/lib/x86_64-linux-gnu/libc.so.6(__libc_start_main+0xed)[0x7f603109176d]
./ProteinShop[0x464df1]
======= Memory map: ========
00400000-00552000 r-xp 00000000 08:07 1715583 /home/case/Downloads/ProteinShop/bin/ProteinShop
00751000-00752000 r--p 00151000 08:07 1715583 /home/case/Downloads/ProteinShop/bin/ProteinShop
00752000-00757000 rw-p 00152000 08:07 1715583 /home/case/Downloads/ProteinShop/bin/ProteinShop
00757000-0079a000 rw-p 00000000 00:00 0
019ad000-019ce000 rw-p 00000000 00:00 0 [heap]
7f602e369000-7f602e37f000 r-xp 00000000 08:07 10751612 /lib/x86_64-linux-gnu/libz.so.1.2.3.4
7f602e37f000-7f602e57e000 ---p 00016000 08:07 10751612 /lib/x86_64-linux-gnu/libz.so.1.2.3.4
7f602e57e000-7f602e57f000 r--p 00015000 08:07 10751612 /lib/x86_64-linux-gnu/libz.so.1.2.3.4
7f602e57f000-7f602e580000 rw-p 00016000 08:07 10751612 /lib/x86_64-linux-gnu/libz.so.1.2.3.4
7f602e580000-7f602e587000 r-xp 00000000 08:07 10751608 /lib/x86_64-linux-gnu/librt-2.15.so
7f602e587000-7f602e786000 ---p 00007000 08:07 10751608 /lib/x86_64-linux-gnu/librt-2.15.so
7f602e786000-7f602e787000 r--p 00006000 08:07 10751608 /lib/x86_64-linux-gnu/librt-2.15.so
7f602e787000-7f602e788000 rw-p 00007000 08:07 10751608 /lib/x86_64-linux-gnu/librt-2.15.so
7f602e788000-7f602e78d000 r-xp 00000000 08:07 2623571 /usr/lib/x86_64-linux-gnu/libXdmcp.so.6.0.0
7f602e78d000-7f602e98c000 ---p 00005000 08:07 2623571 /usr/lib/x86_64-linux-gnu/libXdmcp.so.6.0.0
7f602e98c000-7f602e98d000 r--p 00004000 08:07 2623571 /usr/lib/x86_64-linux-gnu/libXdmcp.so.6.0.0
7f602e98d000-7f602e98e000 rw-p 00005000 08:07 2623571 /usr/lib/x86_64-linux-gnu/libXdmcp.so.6.0.0
7f602e98e000-7f602e990000 r-xp 00000000 08:07 2623568 /usr/lib/x86_64-linux-gnu/libXau.so.6.0.0
7f602e990000-7f602eb8f000 ---p 00002000 08:07 2623568 /usr/lib/x86_64-linux-gnu/libXau.so.6.0.0
7f602eb8f000-7f602eb90000 r--p 00001000 08:07 2623568 /usr/lib/x86_64-linux-gnu/libXau.so.6.0.0
7f602eb90000-7f602eb91000 rw-p 00002000 08:07 2623568 /usr/lib/x86_64-linux-gnu/libXau.so.6.0.0
7f602eb91000-7f602ebb8000 r-xp 00000000 08:07 10747931 /lib/x86_64-linux-gnu/libexpat.so.1.5.2
7f602ebb8000-7f602edb8000 ---p 00027000 08:07 10747931 /lib/x86_64-linux-gnu/libexpat.so.1.5.2
7f602edb8000-7f602edba000 r--p 00027000 08:07 10747931 /lib/x86_64-linux-gnu/libexpat.so.1.5.2
7f602edba000-7f602edbb000 rw-p 00029000 08:07 10747931 /lib/x86_64-linux-gnu/libexpat.so.1.5.2
7f602edbb000-7f602edc4000 r-xp 00000000 08:07 2624341 /usr/lib/x86_64-linux-gnu/libXrender.so.1.3.0
7f602edc4000-7f602efc3000 ---p 00009000 08:07 2624341 /usr/lib/x86_64-linux-gnu/libXrender.so.1.3.0
7f602efc3000-7f602efc4000 r--p 00008000 08:07 2624341 /usr/lib/x86_64-linux-gnu/libXrender.so.1.3.0
7f602efc4000-7f602efc5000 rw-p 00009000 08:07 2624341 /usr/lib/x86_64-linux-gnu/libXrender.so.1.3.0
7f602efc5000-7f602f05b000 r-xp 00000000 08:07 2637478 /usr/lib/x86_64-linux-gnu/libfreetype.so.6.8.0
7f602f05b000-7f602f25a000 ---p 00096000 08:07 2637478 /usr/lib/x86_64-linux-gnu/libfreetype.so.6.8.0
7f602f25a000-7f602f260000 r--p 00095000 08:07 2637478 /usr/lib/x86_64-linux-gnu/libfreetype.so.6.8.0
7f602f260000-7f602f261000 rw-p 0009b000 08:07 2637478 /usr/lib/x86_64-linux-gnu/libfreetype.so.6.8.0
7f602f261000-7f602f26b000 r-xp 00000000 08:07 2621735 /usr/lib/x86_64-linux-gnu/libdrm.so.2.4.0
7f602f26b000-7f602f46a000 ---p 0000a000 08:07 2621735 /usr/lib/x86_64-linux-gnu/libdrm.so.2.4.0
7f602f46a000-7f602f46b000 r--p 00009000 08:07 2621735 /usr/lib/x86_64-linux-gnu/libdrm.so.2.4.0
7f602f46b000-7f602f46c000 rw-p 0000a000 08:07 2621735 /usr/lib/x86_64-linux-gnu/libdrm.so.2.4.0
7f602f46c000-7f602f470000 r-xp 00000000 08:07 2623970 /usr/lib/x86_64-linux-gnu/libXxf86vm.so.1.0.0
7f602f470000-7f602f66f000 ---p 00004000 08:07 2623970 /usr/lib/x86_64-linux-gnu/libXxf86vm.so.1.0.0
7f602f66f000-7f602f670000 r--p 00003000 08:07 2623970 /usr/lib/x86_64-linux-gnu/libXxf86vm.so.1.0.0
7f602f670000-7f602f671000 rw-p 00004000 08:07 2623970 /usr/lib/x86_64-linux-gnu/libXxf86vm.so.1.0.0
7f602f671000-7f602f68e000 r-xp 00000000 08:07 2623538 /usr/lib/x86_64-linux-gnu/libxcb.so.1.1.0
7f602f68e000-7f602f88d000 ---p 0001d000 08:07 2623538 /usr/lib/x86_64-linux-gnu/libxcb.so.1.1.0
7f602f88d000-7f602f88e000 r--p 0001c000 08:07 2623538 /usr/lib/x86_64-linux-gnu/libxcb.so.1.1.0
7f602f88e000-7f602f88f000 rw-p 0001d000 08:07 2623538 /usr/lib/x86_64-linux-gnu/libxcb.so.1.1.0
7f602f88f000-7f602f892000 r-xp 00000000 08:07 2623817 /usr/lib/x86_64-linux-gnu/libxcb-dri2.so.0.0.0
7f602f892000-7f602fa92000 ---p 00003000 08:07 2623817 /usr/lib/x86_64-linux-gnu/libxcb-dri2.so.0.0.0
7f602fa92000-7f602fa93000 r--p 00003000 08:07 2623817 /usr/lib/x86_64-linux-gnu/libxcb-dri2.so.0.0.0
7f602fa93000-7f602fa94000 rw-p 00004000 08:07 2623817 /usr/lib/x86_64-linux-gnu/libxcb-dri2.so.0.0.0
7f602fa94000-7f602faa9000 r-xp 00000000 08:07 2623820 /usr/lib/x86_64-linux-gnu/libxcb-glx.so.0.0.0
7f602faa9000-7f602fca8000 ---p 00015000 08:07 2623820 /usr/lib/x86_64-linux-gnu/libxcb-glx.so.0.0.0
7f602fca8000-7f602fcaa000 r--p 00014000 08:07 2623820 /usr/lib/x86_64-linux-gnu/libxcb-glx.so.0.0.0
7f602fcaa000-7f602fcab000 rw-p 00016000 08:07 2623820 /usr/lib/x86_64-linux-gnu/libxcb-glx.so.0.0.0
7f602fcab000-7f602fcac000 r-xp 00000000 08:07 2622604 /usr/lib/x86_64-linux-gnu/libX11-xcb.so.1.0.0
7f602fcac000-7f602feab000 ---p 00001000 08:07 2622604 /usr/lib/x86_64-linux-gnu/libX11-xcb.so.1.0.0
7f602feab000-7f602feac000 r--p 00000000 08:07 2622604 /usr/lib/x86_64-linux-gnu/libX11-xcb.so.1.0.0
7f602feac000-7f602fead000 rw-p 00001000 08:07 2622604 /usr/lib/x86_64-linux-gnu/libX11-xcb.so.1.0.0
7f602fead000-7f602feb2000 r-xp 00000000 08:07 2623824 /usr/lib/x86_64-linux-gnu/libXfixes.so.3.1.0
7f602feb2000-7f60300b1000 ---p 00005000 08:07 2623824 /usr/lib/x86_64-linux-gnu/libXfixes.so.3.1.0
7f60300b1000-7f60300b2000 r--p 00004000 08:07 2623824 /usr/lib/x86_64-linux-gnu/libXfixes.so.3.1.0
7f60300b2000-7f60300b3000 rw-p 00005000 08:07 2623824 /usr/lib/x86_64-linux-gnu/libXfixes.so.3.1.0
7f60300b3000-7f60300b5000 r-xp 00000000 08:07 2627761 /usr/lib/x86_64-linux-gnu/libXdamage.so.1.1.0
7f60300b5000-7f60302b4000 ---p 00002000 08:07 2627761 /usr/lib/x86_64-linux-gnu/libXdamage.so.1.1.0
7f60302b4000-7f60302b5000 r--p 00001000 08:07 2627761 /usr/lib/x86_64-linux-gnu/libXdamage.so.1.1.0
7f60302b5000-7f60302b6000 rw-p 00002000 08:07 2627761 /usr/lib/x86_64-linux-gnu/libXdamage.so.1.1.0
7f60302b6000-7f60302d7000 r-xp 00000000 08:07 2623025 /usr/lib/x86_64-linux-gnu/libglapi.so.0.0.0
7f60302d7000-7f60304d7000 ---p 00021000 08:07 2623025 /usr/lib/x86_64-linux-gnu/libglapi.so.0.0.0
7f60304d7000-7f60304da000 r--p 00021000 08:07 2623025 /usr/lib/x86_64-linux-gnu/libglapi.so.0.0.0
7f60304da000-7f60304db000 rw-p 00024000 08:07 2623025 /usr/lib/x86_64-linux-gnu/libglapi.so.0.0.0
7f60304db000-7f60304dc000 rw-p 00000000 00:00 0
7f60304dc000-7f60304de000 r-xp 00000000 08:07 2627763 /usr/lib/x86_64-linux-gnu/libXinerama.so.1.0.0
7f60304de000-7f60306dd000 ---p 00002000 08:07 2627763 /usr/lib/x86_64-linux-gnu/libXinerama.so.1.0.0
7f60306dd000-7f60306de000 r--p 00001000 08:07 2627763 /usr/lib/x86_64-linux-gnu/libXinerama.so.1.0.0
7f60306de000-7f60306df000 rw-p 00002000 08:07 2627763 /usr/lib/x86_64-linux-gnu/libXinerama.so.1.0.0
7f60306df000-7f6030713000 r-xp 00000000 08:07 2623967 /usr/lib/x86_64-linux-gnu/libfontconfig.so.1.4.4
7f6030713000-7f6030913000 ---p 00034000 08:07 2623967 /usr/lib/x86_64-linux-gnu/libfontconfig.so.1.4.4
7f6030913000-7f6030914000 r--p 00034000 08:07 2623967 /usr/lib/x86_64-linux-gnu/libfontconfig.so.1.4.4
7f6030914000-7f6030915000 rw-p 00035000 08:07 2623967 /usr/lib/x86_64-linux-gnu/libfontconfig.so.1.4.4
7f6030915000-7f6030929000 r-xp 00000000 08:07 2624886 /usr/lib/x86_64-linux-gnu/libXft.so.2.2.0
7f6030929000-7f6030b28000 ---p 00014000 08:07 2624886 /usr/lib/x86_64-linux-gnu/libXft.so.2.2.0
7f6030b28000-7f6030b29000 r--p 00013000 08:07 2624886 /usr/lib/x86_64-linux-gnu/libXft.so.2.2.0
7f6030b29000-7f6030b2a000 rw-p 00014000 08:07 2624886 /usr/lib/x86_64-linux-gnu/libXft.so.2.2.0
7f6030b2a000-7f6030b3a000 r-xp 00000000 08:07 2627550 /usr/lib/x86_64-linux-gnu/libXext.so.6.4.0
7f6030b3a000-7f6030d39000 ---p 00010000 08:07 2627550 /usr/lib/x86_64-linux-gnu/libXext.so.6.4.0
7f6030d39000-7f6030d3a000 r--p 0000f000 08:07 2627550 /usr/lib/x86_64-linux-gnu/libXext.so.6.4.0
7f6030d3a000-7f6030d3b000 rw-p 00010000 08:07 2627550 /usr/lib/x86_64-linux-gnu/libXext.so.6.4.0
7f6030d3b000-7f6030e6b000 r-xp 00000000 08:07 2623557 /usr/lib/x86_64-linux-gnu/libX11.so.6.3.0
7f6030e6b000-7f603106b000 ---p 00130000 08:07 2623557 /usr/lib/x86_64-linux-gnu/libX11.so.6.3.0
7f603106b000-7f603106c000 r--p 00130000 08:07 2623557 /usr/lib/x86_64-linux-gnu/libX11.so.6.3.0
7f603106c000-7f6031070000 rw-p 00131000 08:07 2623557 /usr/lib/x86_64-linux-gnu/libX11.so.6.3.0
7f6031070000-7f6031225000 r-xp 00000000 08:07 10751589 /lib/x86_64-linux-gnu/libc-2.15.so
7f6031225000-7f6031424000 ---p 001b5000 08:07 10751589 /lib/x86_64-linux-gnu/libc-2.15.so
7f6031424000-7f6031428000 r--p 001b4000 08:07 10751589 /lib/x86_64-linux-gnu/libc-2.15.so
7f6031428000-7f603142a000 rw-p 001b8000 08:07 10751589 /lib/x86_64-linux-gnu/libc-2.15.so
7f603142a000-7f603142f000 rw-p 00000000 00:00 0
7f603142f000-7f6031444000 r-xp 00000000 08:07 10747908 /lib/x86_64-linux-gnu/libgcc_s.so.1
7f6031444000-7f6031643000 ---p 00015000 08:07 10747908 /lib/x86_64-linux-gnu/libgcc_s.so.1
7f6031643000-7f6031644000 r--p 00014000 08:07 10747908 /lib/x86_64-linux-gnu/libgcc_s.so.1
7f6031644000-7f6031645000 rw-p 00015000 08:07 10747908 /lib/x86_64-linux-gnu/libgcc_s.so.1
7f6031645000-7f6031740000 r-xp 00000000 08:07 10751733 /lib/x86_64-linux-gnu/libm-2.15.so
7f6031740000-7f603193f000 ---p 000fb000 08:07 10751733 /lib/x86_64-linux-gnu/libm-2.15.so
7f603193f000-7f6031940000 r--p 000fa000 08:07 10751733 /lib/x86_64-linux-gnu/libm-2.15.so
7f6031940000-7f6031941000 rw-p 000fb000 08:07 10751733 /lib/x86_64-linux-gnu/libm-2.15.so
7f6031941000-7f6031a23000 r-xp 00000000 08:07 2625892 /usr/lib/x86_64-linux-gnu/libstdc++.so.6.0.16
7f6031a23000-7f6031c22000 ---p 000e2000 08:07 2625892 /usr/lib/x86_64-linux-gnu/libstdc++.so.6.0.16
7f6031c22000-7f6031c2a000 r--p 000e1000 08:07 2625892 /usr/lib/x86_64-linux-gnu/libstdc++.so.6.0.16
7f6031c2a000-7f6031c2c000 rw-p 000e9000 08:07 2625892 /usr/lib/x86_64-linux-gnu/libstdc++.so.6.0.16
7f6031c2c000-7f6031c41000 rw-p 00000000 00:00 0
7f6031c41000-7f6031c43000 r-xp 00000000 08:07 10747985 /lib/x86_64-linux-gnu/libdl-2.15.so
7f6031c43000-7f6031e43000 ---p 00002000 08:07 10747985 /lib/x86_64-linux-gnu/libdl-2.15.so
7f6031e43000-7f6031e44000 r--p 00002000 08:07 10747985 /lib/x86_64-linux-gnu/libdl-2.15.so
7f6031e44000-7f6031e45000 rw-p 00003000 08:07 10747985 /lib/x86_64-linux-gnu/libdl-2.15.so
7f6031e45000-7f6031e5d000 r-xp 00000000 08:07 10751591 /lib/x86_64-linux-gnu/libpthread-2.15.so
7f6031e5d000-7f603205c000 ---p 00018000 08:07 10751591 /lib/x86_64-linux-gnu/libpthread-2.15.so
7f603205c000-7f603205d000 r--p 00017000 08:07 10751591 /lib/x86_64-linux-gnu/libpthread-2.15.so
7f603205d000-7f603205e000 rw-p 00018000 08:07 10751591 /lib/x86_64-linux-gnu/libpthread-2.15.so
7f603205e000-7f6032062000 rw-p 00000000 00:00 0
7f6032062000-7f60320be000 r-xp 00000000 08:07 3017177 /usr/lib/x86_64-linux-gnu/mesa/libGL.so.1.2.0
7f60320be000-7f60322be000 ---p 0005c000 08:07 3017177 /usr/lib/x86_64-linux-gnu/mesa/libGL.so.1.2.0
7f60322be000-7f60322c0000 r--p 0005c000 08:07 3017177 /usr/lib/x86_64-linux-gnu/mesa/libGL.so.1.2.0
7f60322c0000-7f60322c1000 rw-p 0005e000 08:07 3017177 /usr/lib/x86_64-linux-gnu/mesa/libGL.so.1.2.0
7f60322c1000-7f60322c2000 rw-p 00000000 00:00 0
7f60322c2000-7f60323ed000 r-xp 00000000 08:07 2629023 /usr/lib/x86_64-linux-gnu/libfltk.so.1.3
7f60323ed000-7f60325ed000 ---p 0012b000 08:07 2629023 /usr/lib/x86_64-linux-gnu/libfltk.so.1.3
7f60325ed000-7f60325f2000 r--p 0012b000 08:07 2629023 /usr/lib/x86_64-linux-gnu/libfltk.so.1.3
7f60325f2000-7f60325f8000 rw-p 00130000 08:07 2629023 /usr/lib/x86_64-linux-gnu/libfltk.so.1.3
7f60325f8000-7f60325fe000 rw-p 00000000 00:00 0
7f60325fe000-7f6032617000 r-xp 00000000 08:07 2629031 /usr/lib/x86_64-linux-gnu/libfltk_gl.so.1.3
7f6032617000-7f6032817000 ---p 00019000 08:07 2629031 /usr/lib/x86_64-linux-gnu/libfltk_gl.so.1.3
7f6032817000-7f603281a000 r--p 00019000 08:07 2629031 /usr/lib/x86_64-linux-gnu/libfltk_gl.so.1.3
7f603281a000-7f603281c000 rw-p 0001c000 08:07 2629031 /usr/lib/x86_64-linux-gnu/libfltk_gl.so.1.3
7f603281c000-7f603283e000 r-xp 00000000 08:07 10753193 /lib/x86_64-linux-gnu/ld-2.15.so
7f60329f5000-7f6032a05000 rw-p 00000000 00:00 0
7f6032a3a000-7f6032a3e000 rw-p 00000000 00:00 0
7f6032a3e000-7f6032a3f000 r--p 00022000 08:07 10753193 /lib/x86_64-linux-gnu/ld-2.15.so
7f6032a3f000-7f6032a41000 rw-p 00023000 08:07 10753193 /lib/x86_64-linux-gnu/ld-2.15.so
7fffe7499000-7fffe74ba000 rw-p 00000000 00:00 0 [stack]
7fffe75ff000-7fffe7600000 r-xp 00000000 00:00 0 [vdso]
ffffffffff600000-ffffffffff601000 r-xp 00000000 00:00 0 [vsyscall]
Aborted (core dumped)
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Nathan McCorkle
Sep 20, 2013, 6:31:55 PM9/20/13
to diybio
did you change the compile flag and make clean && make?
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Cathal Garvey
Sep 20, 2013, 6:41:23 PM9/20/13
to diy...@googlegroups.com
Awesome stuff, thanks Tim! :)
On Fri, 20 Sep 2013 11:45:05 -1000
> >>>>>> http://www.rcsb.org/pdb/**explore.do?structureId=1UBQ<http://www.rcsb.org/pdb/explore.do?structureId=1UBQ>
> >>>>>>>>>> TerItFix.cgi<http://godzilla.uchicago.edu/cgi-bin/aashish2/TerItFix/TerItFix.cgi>
> >>>>>>>>>> forum/diybio?hl=en<https://groups.google.com/d/forum/diybio?hl=en>
> >>>>>>>>>> 4be5-a34c-965f1cc40e78%**40googlegroups.com<https://groups.google.com/d/msgid/diybio/61991497-b141-4be5-a34c-965f1cc40e78%40googlegroups.com>
> >>>>>>>>>> .
> >>>>>>>>>>
> >>>>>>>>>> For more options, visit https://groups.google.com/**
> >>>>>>>>>> groups/opt_out <https://groups.google.com/groups/opt_out>.
> >>>>>>>>> 3DZGspmo1mn4KcUuiggJmakRdWgcRs**c2_WkjZJxgA-gBA%40mail.gmail.**com<https://groups.google.com/d/msgid/diybio/CAAcUL6%3DZGspmo1mn4KcUuiggJmakRdWgcRsc2_WkjZJxgA-gBA%40mail.gmail.com>
> >>>>>>>>> .
> >>>>>>>>>
> >>>>>>>>> For more options, visit
> >>>>>>>>> https://groups.google.com/**groups/opt_out<https://groups.google.com/groups/opt_out> .
> >>>>>>>> CAEUkM4tqaUpHcJfc8kqkdriS-**n9KN2JDvGuHvOyK2uVs%2BYLUVQ%**
> >>>>>>>> 40mail.gmail.com<https://groups.google.com/d/msgid/diybio/CAEUkM4tqaUpHcJfc8kqkdriS-n9KN2JDvGuHvOyK2uVs%2BYLUVQ%40mail.gmail.com>
> >>>>>>>> .
> >>>>>>>>
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> >>>>>>> topic/diybio/nlpw_IuesRY/**unsubscribe<https://groups.google.com/d/topic/diybio/nlpw_IuesRY/unsubscribe> .
> >>>>>>> 3D1qvPs4qCk0ob_**7zBdknyWTVwNNBM8HsopMPQR%**2BsUg%40mail.gmail.com<https://groups.google.com/d/msgid/diybio/CAAcUL6k%3D%3D1qvPs4qCk0ob_7zBdknyWTVwNNBM8HsopMPQR%2BsUg%40mail.gmail.com>
> >>>>>>> .
> >>>>>>>
> >>>>>>> For more options, visit
> >>>>>>> https://groups.google.com/**groups/opt_out<https://groups.google.com/groups/opt_out> .
> >>>>>> **msgid/diybio/**CAEUkM4vKvvxZ4FLgDMUa9wCH%**
> >>>>>> 3DbXSGuMkK5fb4bF1pNhzEngOzw%**40mail.gmail.com<https://groups.google.com/d/msgid/diybio/CAEUkM4vKvvxZ4FLgDMUa9wCH%3DbXSGuMkK5fb4bF1pNhzEngOzw%40mail.gmail.com> .
> >>>>>>
> >>>>>> For more options, visit
> >>>>>> https://groups.google.com/**groups/opt_out<https://groups.google.com/groups/opt_out> .
> >>>> .
> >>> .
> >> .
> > .
On Fri, 20 Sep 2013 11:45:05 -1000
> >>>>>>
> >>>>>>
> >>>>>> On Thu, Sep 19, 2013 at 9:20 PM, William Heath
> >>>>>> <wgh...@gmail.com>wrote:
> >>>>>>
> >>>>>>> Hi All,
> >>>>>>>
> >>>>>>> It segfaulted reading the pdb. Here is the output:
> >>>>>>>
> >>>>>>> http://pastebin.com/k8ciJnzy
> >>>>>>>
> >>>>>>> Is there another simpler pdb it could read you think?
> >>>>>>>
> >>>>>>> -Tim
> >>>>>>>
> >>>>>>> P.S.
> >>>>>>>
> >>>>>>> I just removed all code from void
> >>>>>>> GLLineIlluminator::**enableLighting(GLContextData&
> >>>>>>
> >>>>>> On Thu, Sep 19, 2013 at 9:20 PM, William Heath
> >>>>>> <wgh...@gmail.com>wrote:
> >>>>>>
> >>>>>>> Hi All,
> >>>>>>>
> >>>>>>> It segfaulted reading the pdb. Here is the output:
> >>>>>>>
> >>>>>>> http://pastebin.com/k8ciJnzy
> >>>>>>>
> >>>>>>> Is there another simpler pdb it could read you think?
> >>>>>>>
> >>>>>>> -Tim
> >>>>>>>
> >>>>>>> P.S.
> >>>>>>>
> >>>>>>> I just removed all code from void
> >>>>>>> contextData) const to get it to compile. I will fix that
> >>>>>>> later, just want to see what is possible.
> >>>>>>>
> >>>>>>>
> >>>>>>> On Thu, Sep 19, 2013 at 4:10 PM, Josiah Zayner
> >>>>>>> <josiah...@gmail.com>wrote:
> >>>>>>>
> >>>>>>>> www.rcsb.org
> >>>>>>>>
> >>>>>>>> What did you do?
> >>>>>>>>
> >>>>>>>>
> >>>>>>>> On Thu, Sep 19, 2013 at 9:08 PM, William Heath
> >>>>>>>> <wgh...@gmail.com>wrote:
> >>>>>>>>
> >>>>>>>>> Hi All,
> >>>>>>>>>
> >>>>>>>>> I got it to compile! Here is a screenshot of it running:
> >>>>>>>>>
> >>>>>>>>> http://imagebin.org/271404
> >>>>>>>>>
> >>>>>>>>> Where can I get a pdb file or .pred file to test that it
> >>>>>>>>> works?
> >>>>>>>>>
> >>>>>>>>> -Tim
> >>>>>>>>>
> >>>>>>>>>
> >>>>>>>>> On Thu, Sep 19, 2013 at 3:59 PM, Josiah Zayner <
> >>>>>>>>> josiah...@gmail.com> wrote:
> >>>>>>>>>
> >>>>>>>>>> The code appears broke beyond brokenness. The website is
> >>>>>>>>>> down
> >>>>>>>>>> http://proteinshop.lbl.gov/**Index.html<http://proteinshop.lbl.gov/Index.html>.
> >>>>>>> later, just want to see what is possible.
> >>>>>>>
> >>>>>>>
> >>>>>>> On Thu, Sep 19, 2013 at 4:10 PM, Josiah Zayner
> >>>>>>> <josiah...@gmail.com>wrote:
> >>>>>>>
> >>>>>>>> www.rcsb.org
> >>>>>>>>
> >>>>>>>> What did you do?
> >>>>>>>>
> >>>>>>>>
> >>>>>>>> On Thu, Sep 19, 2013 at 9:08 PM, William Heath
> >>>>>>>> <wgh...@gmail.com>wrote:
> >>>>>>>>
> >>>>>>>>> Hi All,
> >>>>>>>>>
> >>>>>>>>> I got it to compile! Here is a screenshot of it running:
> >>>>>>>>>
> >>>>>>>>> http://imagebin.org/271404
> >>>>>>>>>
> >>>>>>>>> Where can I get a pdb file or .pred file to test that it
> >>>>>>>>> works?
> >>>>>>>>>
> >>>>>>>>> -Tim
> >>>>>>>>>
> >>>>>>>>>
> >>>>>>>>> On Thu, Sep 19, 2013 at 3:59 PM, Josiah Zayner <
> >>>>>>>>> josiah...@gmail.com> wrote:
> >>>>>>>>>
> >>>>>>>>>> The code appears broke beyond brokenness. The website is
> >>>>>>>>>> down
> >>>>>>>>>> I would try emaling Sylvia at SNCrivelli [at] lbl.gov if
> >>>>>>>>>> you really want to try and get it working. However.
> >>>>>>>>>>
> >>>>>>>>>> If you want to do similar stuff I would install VMD
> >>>>>>>>>> http://www.ks.uiuc.edu/**Research/vmd/<http://www.ks.uiuc.edu/Research/vmd/>
> >>>>>>>>>> you really want to try and get it working. However.
> >>>>>>>>>>
> >>>>>>>>>> If you want to do similar stuff I would install VMD
> >>>>>>>>>> or pymol: sudo apt-get install pymol
> >>>>>>>>>>
> >>>>>>>>>> for secondary structure prediction try PSIPRED:
> >>>>>>>>>> http://bioinf.cs.ucl.**ac.uk/psipred/<http://bioinf.cs.ucl.ac.uk/psipred/>
> >>>>>>>>>>
> >>>>>>>>>> for secondary structure prediction try PSIPRED:
> >>>>>>>>>>
> >>>>>>>>>> And for protein structure prediction use:
> >>>>>>>>>> http://swissmodel.expasy.**org/
> >>>>>>>>>> And for protein structure prediction use:
> >>>>>>>>>> <http://swissmodel.expasy.org/> if it has some homology to
> >>>>>>>>>> some other structure
> >>>>>>>>>>
> >>>>>>>>>> or
> >>>>>>>>>> http://godzilla.uchicago.**edu/cgi-bin/aashish2/TerItFix/**
> >>>>>>>>>> some other structure
> >>>>>>>>>>
> >>>>>>>>>> or
> >>>>>>>>>> TerItFix.cgi<http://godzilla.uchicago.edu/cgi-bin/aashish2/TerItFix/TerItFix.cgi>
> >>>>>>>>>> if it does not have any homology
> >>>>>>>>>>
> >>>>>>>>>> for Molecular Dynamics Simulations try namd which comes
> >>>>>>>>>> with VMD or gromacs: sudo apt-get install gromacs
> >>>>>>>>>>
> >>>>>>>>>>
> >>>>>>>>>>
> >>>>>>>>>> On Thursday, September 19, 2013 7:46:59 AM UTC-5, John
> >>>>>>>>>> Dohnal wrote:
> >>>>>>>>>>>
> >>>>>>>>>>> I have never used a Linux OS before, but I downloaded the
> >>>>>>>>>>> latest version of Ubuntu in order to run Protein Shop. I
> >>>>>>>>>>> downloaded the latest version of Protein Shop, but I
> >>>>>>>>>>> don't know how to start it. I know nothing about using
> >>>>>>>>>>> Linux, so any explicit, basic instructions would be most
> >>>>>>>>>>> helpful. In the readme file, it mentions some other
> >>>>>>>>>>> files that may need to be installed, but I don't even
> >>>>>>>>>>> know where to begin. Please help!
> >>>>>>>>>>>
> >>>>>>>>>>> Thanks,
> >>>>>>>>>>> John
> >>>>>>>>>>>
> >>>>>>>>>> --
> >>>>>>>>>> -- You received this message because you are subscribed to
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> >>>>>>>>>> send email to diy...@googlegroups.com. To unsubscribe from
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> >>>>>>>>>>
> >>>>>>>>>> for Molecular Dynamics Simulations try namd which comes
> >>>>>>>>>> with VMD or gromacs: sudo apt-get install gromacs
> >>>>>>>>>>
> >>>>>>>>>>
> >>>>>>>>>>
> >>>>>>>>>> On Thursday, September 19, 2013 7:46:59 AM UTC-5, John
> >>>>>>>>>> Dohnal wrote:
> >>>>>>>>>>>
> >>>>>>>>>>> I have never used a Linux OS before, but I downloaded the
> >>>>>>>>>>> latest version of Ubuntu in order to run Protein Shop. I
> >>>>>>>>>>> downloaded the latest version of Protein Shop, but I
> >>>>>>>>>>> don't know how to start it. I know nothing about using
> >>>>>>>>>>> Linux, so any explicit, basic instructions would be most
> >>>>>>>>>>> helpful. In the readme file, it mentions some other
> >>>>>>>>>>> files that may need to be installed, but I don't even
> >>>>>>>>>>> know where to begin. Please help!
> >>>>>>>>>>>
> >>>>>>>>>>> Thanks,
> >>>>>>>>>>> John
> >>>>>>>>>>>
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William Heath
Sep 20, 2013, 6:49:40 PM9/20/13
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Hi Nathan,
I am new to creating virtual appliances. I didn't know I needed to export the virtual appliance to get it to save the files I put on it etc... Doing that now and will re-upload to my server so people can download it if they want.
-Tim
P.S.
Sorry about that and thanks for your patience :>
Josiah Zayner
Sep 20, 2013, 7:05:25 PM9/20/13
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Yeah yeah ok works now. Didn't make clean. Sweet tested out some of the structure distortion functions. Looks pretty awesome.
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Nathan McCorkle
Sep 20, 2013, 7:10:18 PM9/20/13
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I tried a klenow fragment and it crashed but ubiquitin works. I'll look into making a debian package this weekend.
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William Heath
Sep 20, 2013, 7:22:16 PM9/20/13
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Hi Nathan and Josiah,
Can you please commit changes and add to the readme/wiki on github?
-Tim
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Nathan McCorkle
Sep 22, 2013, 5:30:50 AM9/22/13
to diybio
On Fri, Sep 20, 2013 at 4:22 PM, William Heath <wgh...@gmail.com> wrote:
> Hi Nathan and Josiah,
>
> Can you please commit changes and add to the readme/wiki on github?
Ok, tested this on a 32 bit ubuntu and 64bit debian machine, updated
> Hi Nathan and Josiah,
>
> Can you please commit changes and add to the readme/wiki on github?
the README for easy install.
https://github.com/nmz787/ProteinShop
here's a compressed version of the same thing:
http://diyhpl.us/~nmz787/ProteinShop_3.1.1_ubuntu_debian.tar.gz
I will try to figure out how to package it into a .deb, but since I
used those g77 .deb files Josiah pointed me to (which are now on the
github repo) I'm not sure how easy it will be to package other
packages!
Meredith L. Patterson
Sep 22, 2013, 11:26:21 AM9/22/13
to DIYBio Mailing List
Hi Nathan,
I'm trying to compile your repo on a debian x86_64 box, but for some reason it keeps dying with the same linker error: "undefined reference to `_glapi_tls_Dispatch'". I've updated libglapi-mesa per http://stackoverflow.com/questions/18348726/not-able-to-compile-gtk-program, but still no love. Any ideas?
The one thing I'm doing differently is I swapped out g77 for gfortran in the Makefile -- if someone's already tried that, I missed it. But since this seems to be an unrelated problem on my end, you might try apt-get installing gfortran and swapping out "FC = g77" for "FC = gfortran" on line 508 of the Makefile and see if that removes the need for the old g77 deps.
Cheers,
--mlp
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Cathal Garvey (Phone)
Sep 22, 2013, 12:16:39 PM9/22/13
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There was fortran in there? How did I miss that?!
"Meredith L. Patterson" <clon...@gmail.com> wrote:
--
Sent from my Android device with K-9 Mail. Please excuse my brevity.
Nathan McCorkle
Sep 22, 2013, 12:41:41 PM9/22/13
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I tried fort77 before Josiah posted the g77 link, which I added to the github repo, there is a 64 bit version.
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Meredith L. Patterson
Sep 22, 2013, 12:49:00 PM9/22/13
to DIYBio Mailing List
The thing is, g77 is deprecated and has been replaced with gfortran. So if it builds with gfortran, then you can just add that to the dependencies list and not have to bother with a repo full of debs.
Cheers,
--mlp
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Nathan McCorkle
Sep 22, 2013, 1:16:00 PM9/22/13
to diybio
I'll try to bang on it some more later today/tonight.
On Sun, Sep 22, 2013 at 9:49 AM, Meredith L. Patterson
> https://groups.google.com/d/msgid/diybio/CAPxGCxdYqVp7FVFdQLm8Bkh1LwS2%2B7u93prqi-ntituzT%3DpCLQ%40mail.gmail.com.
-Nathan
On Sun, Sep 22, 2013 at 9:49 AM, Meredith L. Patterson
-Nathan
Josiah Zayner
Sep 22, 2013, 1:55:55 PM9/22/13
to diy...@googlegroups.com
I tried switching the FORTRAN compiler to gfortran and it compiled just fine for me.
This is on Ubuntu 12.04.
However, my system is nowhere near a fresh install soooo. Take this how you will.
My only guess for you Meredith is to update gtk and cairo if you can, as these have also been linked to similar problems that you are having in people trying to compile other software.
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Meredith L. Patterson
Sep 22, 2013, 1:59:13 PM9/22/13
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Thanks for checking that out, Josiah! I'll keep fiddling with gtk and see if I can get it working. In the meantime, can you find out what library on your machine provides the symbol `_glapi_tls_Dispatch'?
Cheers,
--mlp
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Josiah Zayner
Sep 22, 2013, 2:40:21 PM9/22/13
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I tried this as root and found nothing... very strange
for i in `find / -name "*.a" -print`; do nm -o $i 2>/dev/null | grep "lapi" | grep -w T; doneIt appears to be a Mesa or GL call. Try updating both of those libraries and development headers maybe?
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Meredith L. Patterson
Sep 22, 2013, 2:57:32 PM9/22/13
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I'd already done an apt-get update/upgrade and that didn't help, but installing libgl1-mesa-swx11 did. Hello ubiquitin! You are very purple.
Nathan, want me to send you a pull request?
Cheers,
--mlp
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Nathan McCorkle
Sep 22, 2013, 5:15:14 PM9/22/13
to diybio
Sure! Will it just be to update the Makefile (gfortran) and README
(for adding libgl1-mesa-swx11)? I haven't accepted changes before,
etc.
On Sun, Sep 22, 2013 at 11:57 AM, Meredith L. Patterson
> https://groups.google.com/d/msgid/diybio/CAPxGCxehm_2g8L4cDFKpAcGh4_gAnm4GwO%3DPMZbVTVzOssW1SQ%40mail.gmail.com.
(for adding libgl1-mesa-swx11)? I haven't accepted changes before,
etc.
On Sun, Sep 22, 2013 at 11:57 AM, Meredith L. Patterson
Meredith L. Patterson
Sep 22, 2013, 5:29:57 PM9/22/13
to DIYBio Mailing List
Yup, that's it (also adding gfortran to the README). I removed the install.sh instructions from the README since the debs aren't necessary anymore, but I'll leave restructuring the repo up to you.
Cheers,
--mlp
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Nathan McCorkle
Sep 22, 2013, 8:38:05 PM9/22/13
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Ok I might be able to test with gfortran tonight if not early tomorrow.
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John Dohnal
Oct 3, 2013, 2:36:59 PM10/3/13
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Is anyone still working on this? Or should I try the other options for protein manipulation?
Thanks,
John
Thanks,
John
Cathal Garvey (Phone)
Oct 3, 2013, 2:42:18 PM10/3/13
to diy...@googlegroups.com
It sounds like the others have got it partially working, though very unstably. I would guess it's "working but impractical" at this stage, and without a strong impetus to improve perhaps that's where it'll stay; I would suggest becoming familiar with alternatives, but perhaps one of the real hackers will chime in with a heartening update?
Nathan McCorkle
Oct 3, 2013, 3:31:02 PM10/3/13
to diybio
John, did you try the instructions I posted on github? I am able to
use it to view proteins in 3D but I didn't look at the documentation
to see what else the software is capable of.
Meredith, I am on github now and don't see any pull requests. I
changed to gfortran and it still compiles and works, I checked and I
DON'T have libgl1-mesa-swx11 installed... so it must be something
else, maybe that got installed along with libgl1-mesa-swx11 for you?
I'm working on making a debian (ubuntu) single-file package that will
install itself. I'll post when I get it to work, or get sick or
trying.
use it to view proteins in 3D but I didn't look at the documentation
to see what else the software is capable of.
Meredith, I am on github now and don't see any pull requests. I
changed to gfortran and it still compiles and works, I checked and I
DON'T have libgl1-mesa-swx11 installed... so it must be something
else, maybe that got installed along with libgl1-mesa-swx11 for you?
I'm working on making a debian (ubuntu) single-file package that will
install itself. I'll post when I get it to work, or get sick or
trying.
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William Heath
Oct 3, 2013, 5:43:24 PM10/3/13
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Hi John,
I am quite interested in assisting you in any way you need. I am a computer scientist that has studied synthetic biology for a number of years. You can download and run protein shop effortlessly using the virtual appliance I created here:
All tools to run this virtual appliance are free. All you have to do is download virtual box and .ova from that website and start the ova appliance. Proteinshop will come up automatically with the ubiquitin protein. Let me know if you have questions :>
-Tim
P.S.
Meredith said she wanted to create a test suite and what have you to make this fully functional. I am happy to assist in that effort! Meredith, please put on your supergirl costume and use me like a tool in your tool box :>
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Reason
Oct 6, 2013, 3:20:19 PM10/6/13
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On 10/03/2013 04:43 PM, William Heath
wrote:
I am quite interested in assisting you in any way you need. I am a computer scientist that has studied synthetic biology for a number of years. You can download and run protein shop effortlessly using the virtual appliance I created here: http://www.graysonconsulting.biz/ All tools to run this virtual appliance are free. All you have to do is download virtual box and .ova from that website and start the ova appliance. Proteinshop will come up automatically with the ubiquitin protein. Let me know if you have questions :>
I have taken this as a reference point and set up a
Vagrant/Virtualbox/Chef arrangement:
https://github.com/exratione/protein-shop-vagrant
This should be a push-button setup for most of you after you get Vagrant, Virtualbox, Chef, and Librarian-chef installed. The docs are hopefully comprehensive enough.
These are 64-bit VMs, so you'll need a 64-bit host OS.
I'm not done with the Ubuntu version yet, so if you want to try it out, use the CentOS box. That works for me: I can get the pretty picture of purple Ubiquitin to show up. More than that I'm not prepared to vouch for.
The issues with g77 are legion, it's a horrible mess trying to get it onto any modern platform, so don't even try to use it. Use gfortran instead and alter the Makefile accordingly. That works fine for me on both Ubuntu and CentOS.
William: I do need to know how, if at all, you altered the ProteinShop codebase from the original so I can add that to the docs. Did you replace the geometry section, as was mentioned earlier in the thread, for example? The ProteinShop code I'm using is pulled from your example VM.
Reason
https://github.com/exratione/protein-shop-vagrant
This should be a push-button setup for most of you after you get Vagrant, Virtualbox, Chef, and Librarian-chef installed. The docs are hopefully comprehensive enough.
These are 64-bit VMs, so you'll need a 64-bit host OS.
I'm not done with the Ubuntu version yet, so if you want to try it out, use the CentOS box. That works for me: I can get the pretty picture of purple Ubiquitin to show up. More than that I'm not prepared to vouch for.
The issues with g77 are legion, it's a horrible mess trying to get it onto any modern platform, so don't even try to use it. Use gfortran instead and alter the Makefile accordingly. That works fine for me on both Ubuntu and CentOS.
William: I do need to know how, if at all, you altered the ProteinShop codebase from the original so I can add that to the docs. Did you replace the geometry section, as was mentioned earlier in the thread, for example? The ProteinShop code I'm using is pulled from your example VM.
Reason
John Dohnal
Oct 8, 2013, 3:37:27 PM10/8/13
to diy...@googlegroups.com
Hi Tim,
Thank you and everyone who contributed to this thread. Unfortunately, I had no idea what any of you were talking about lol! I appreciate you taking the time to get it working. I'm still not sure how to use the information you posted on your website. For instance, I'm not sure where to run the commands for doing the change directory or the make. Never used Linux before, so don't even know where to start. I need "Idiot's Guide to Running Programs in Linux".
Thanks,
John
Thank you and everyone who contributed to this thread. Unfortunately, I had no idea what any of you were talking about lol! I appreciate you taking the time to get it working. I'm still not sure how to use the information you posted on your website. For instance, I'm not sure where to run the commands for doing the change directory or the make. Never used Linux before, so don't even know where to start. I need "Idiot's Guide to Running Programs in Linux".
Thanks,
John
John Dohnal
Oct 8, 2013, 3:45:40 PM10/8/13
to diy...@googlegroups.com
Hi Josiah,
Maybe if I told you what I wanted to do, you could better advise me on which program/s might be better for what I want to do. I have a target molecule as a substrate. By identifying several structures in the molecule, I've identified a number of proteins which have substrates which are similar to the structures in my target molecule. I want to, first, compare the homology of these proteins to find any similar structures. Second, I'd like to be able to "clip" those similar structures and be able to "paste" them together. Lastly, I'd like to see how well the "new" protein fits with my original target molecule. I realize that I will probably need several programs to accomplish this, so if you could explain how each program could perform each portion of my process, that would be awesome.
Thanks,
John
On Thursday, September 19, 2013 9:59:12 PM UTC-4, Josiah Zayner wrote:
Maybe if I told you what I wanted to do, you could better advise me on which program/s might be better for what I want to do. I have a target molecule as a substrate. By identifying several structures in the molecule, I've identified a number of proteins which have substrates which are similar to the structures in my target molecule. I want to, first, compare the homology of these proteins to find any similar structures. Second, I'd like to be able to "clip" those similar structures and be able to "paste" them together. Lastly, I'd like to see how well the "new" protein fits with my original target molecule. I realize that I will probably need several programs to accomplish this, so if you could explain how each program could perform each portion of my process, that would be awesome.
Thanks,
John
On Thursday, September 19, 2013 9:59:12 PM UTC-4, Josiah Zayner wrote:
The code appears broke beyond brokenness. The website is down http://proteinshop.lbl.gov/Index.html. I would try emaling Sylvia at SNCrivelli [at] lbl.gov if you really want to try and get it working. However.If you want to do similar stuff I would install VMD http://www.ks.uiuc.edu/Research/vmd/
or pymol: sudo apt-get install pymol
for secondary structure prediction try PSIPRED: http://bioinf.cs.ucl.ac.uk/psipred/And for protein structure prediction use: http://swissmodel.expasy.org/ if it has some homology to some other structureor http://godzilla.uchicago.edu/cgi-bin/aashish2/TerItFix/TerItFix.cgi if it does not have any homology
for Molecular Dynamics Simulations try namd which comes with VMD or gromacs: sudo apt-get install gromacs
Josiah Zayner
Oct 8, 2013, 4:15:04 PM10/8/13
to diy...@googlegroups.com
All of this can be done through either Windows or Linux.
Next, what you will want to do is a multiple sequence alignment or a pair-wise sequence alignment between the proteins. Depending on if you want to know how each sequence compares to a master sequence (pair-wise) or how each sequence compares to each other(Multiple)
Multiple sequence alignment: http://www.ebi.ac.uk/Tools/msa/clustalo/
These will let you know the % similarity, generally how similar the sequences are to each other.
If you do not have structures for these proteins you can use SWISS MODEL to generate a homology mode if a suitablely similar structure is found: http://swissmodel.expasy.org/
Next download VMD: http://www.ks.uiuc.edu/Development/Download/download.cgi?PackageName=VMD
Load your PDB structures up in VMD: File-> New molecule
Ok now make it all look presentable by going to:
Ok now make it all look presentable by going to:
Graphics->Representations
Drawing Method and choose New Cartoon
Coloring Method Choose ColorID and choose a color
Do this for each protein by using the Selected molecule dropdown box at the top of the Representations window.
Once you have all the structures done
Goto: Extensions -> Analysis-> RMSD calculator
Where is says "residue 5 to 85" change that to the length or your protein. If you don't know the exact length goto: Extensions-> Analysis->Sequence viewer. Try and use as much of the structure as possible or if the region you are interested in is > 20 residues try that first. Next in the RMSD window click Align then click RMSD. RMSD is the Root Mean Square Deviation, basically how different overall the two structures by their positions in 3D space. Low number is good, high number is bad.
Look at the spot where you think the substrate of molecule interacts with the protein(press keyboard S to scale the 3D models, R to rotate and T to translate) and identify the residues by using:
Mouse->Label->Atoms and click on the structure it should give you a residue number and atom name the residue number should be something like "R57"
Go back to the protein sequence alignments and look around these atoms and see if the residues are the same or similar.
If the residues are the same or similar and the RMSD between the structures is small there is a good chance the proteins bind or interact with the same substrate.
If the residues are the same or similar and the RMSD between the structures is small there is a good chance the proteins bind or interact with the same substrate.
More complex analysis can then be done with Molecular Dynamics and docking simulations.
If you have more specific questions or errors please let me know and I will see what I can do to help.
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Cathal Garvey (Phone)
Oct 8, 2013, 4:03:18 PM10/8/13
to diy...@googlegroups.com
Well, usually the idiot's guide is "double click", when it comes to the sort of graphical program people from Applesoft systems are most familiar with. It should be the same for this, too, onve it's built.
The smaller problem lies in that the software you've chosen isn't available "built", only as source code. That's not a linux problem: if this were a winmac app, it would still need to be built first.
The bigger problem is that it's proven really challenging to build, on account of innate bugs and simply becoming outdated.
The smaller problem lies in that the software you've chosen isn't available "built", only as source code. That's not a linux problem: if this were a winmac app, it would still need to be built first.
The bigger problem is that it's proven really challenging to build, on account of innate bugs and simply becoming outdated.
William Heath
Oct 8, 2013, 5:32:53 PM10/8/13
to diy...@googlegroups.com
Hi John,
Here are the steps you need to get proteinshop running on any platform:
1. Download virtual box from here: https://www.virtualbox.org/wiki/Downloads
2. Download the .ova from www.graysonconsutling.biz
3. Open the .ova in virtual box
It will boot up the linux virtual machine and protein shop will automatically start with the ubiquitin protein loaded.
-Tim
P.S.
This is meant to be very easy! :>
To view this discussion on the web visit https://groups.google.com/d/msgid/diybio/573084f6-8b32-4552-aed6-5c001f720827%40googlegroups.com.
John Dohnal
Oct 9, 2013, 9:08:27 AM10/9/13
to diy...@googlegroups.com
Thank you Josiah! I will try these this weekend.
Best,
John
Best,
John
John Dohnal
Oct 9, 2013, 9:10:20 AM10/9/13
to diy...@googlegroups.com, cathal...@cathalgarvey.me
Hi Cathal,
Well, yes, I can see that now after watching you all do battle with this dragon. Please forgive my ignorance and thank you for working on this. I hope you enjoyed the challenge!
Best,
John
Well, yes, I can see that now after watching you all do battle with this dragon. Please forgive my ignorance and thank you for working on this. I hope you enjoyed the challenge!
Best,
John
John Dohnal
Oct 9, 2013, 9:14:24 AM10/9/13
to diy...@googlegroups.com
Thank you Tim! This was exactly what I needed. I will give it a try this weekend.
Best,
John
Best,
John
Brian Degger
Oct 20, 2013, 9:02:47 AM10/20/13
to diy...@googlegroups.com
What is the password on the centos/proteinbox vm?
To view this discussion on the web visit https://groups.google.com/d/msgid/diybio/3ba8ce9c-6b7c-45f8-a507-ae804b715e61%40googlegroups.com.
Reason
Oct 20, 2013, 9:45:20 AM10/20/13
to diy...@googlegroups.com
centos:reverse
Or you can try the Vagrant version:
https://github.com/exratione/protein-shop-vagrant
Where it is vagrant:vagrant
Reason
Or you can try the Vagrant version:
https://github.com/exratione/protein-shop-vagrant
Where it is vagrant:vagrant
Reason
On 10/20/2013 08:02 AM, Brian Degger wrote:
What is the password on the centos/proteinbox vm? On 9 Oct 2013 14:14, "John Dohnal" <johnh...@aol.com> wrote:
Thank you Tim! This was exactly what I needed. I will give it a try this weekend. Best, John On Tuesday, October 8, 2013 5:32:53 PM UTC-4, wgh...@gmail.com wrote:
Hi John, Here are the steps you need to get proteinshop running on any platform: 1. Download virtual box from here: https://www.virtualbox.** org/wiki/Downloads <https://www.virtualbox.org/wiki/Downloads>
2. Download the .ova from www.graysonconsutling.biz 3. Open the .ova in virtual box It will boot up the linux virtual machine and protein shop will automatically start with the ubiquitin protein loaded. -Tim P.S. This is meant to be very easy! :> On Tue, Oct 8, 2013 at 9:37 AM, John Dohnal <johnh...@aol.com> wrote:
Hi Tim, Thank you and everyone who contributed to this thread. Unfortunately, I had no idea what any of you were talking about lol! I appreciate you taking the time to get it working. I'm still not sure how to use the information you posted on your website. For instance, I'm not sure where to run the commands for doing the change directory or the make. Never used Linux before, so don't even know where to start. I need "Idiot's Guide to Running Programs in Linux". Thanks, John On Thursday, October 3, 2013 5:43:24 PM UTC-4, wgh...@gmail.com wrote:
Hi John, I am quite interested in assisting you in any way you need. I am a computer scientist that has studied synthetic biology for a number of years. You can download and run protein shop effortlessly using the virtual appliance I created here:
. To unsubscribe from this group, send email to diybio+un...@**googlegroups.com. For more options, visit this group at https://groups.google.com/d/**fo**rum/diybio?hl=en<https://groups.google.com/d/forum/diybio?hl=en> Learn more at www.diybio.org --- You received this message because you are subscribed to the Google Groups "DIYbio" group. To unsubscribe from this group and stop receiving emails from it, send an email to diybio+un...@**googlegroups.com. To post to this group, send email to diy...@googlegroups.com. Visit this group at http://groups.google.com/**group**/diybio<http://groups.google.com/group/diybio> . To view this discussion on the web visit https://groups.google.com/d/* *ms**gid/diybio/97b817f5-0120-**43d5-**b9d8-8161e063ee87%** 40googlegrou**ps.com<https://groups.google.com/d/msgid/diybio/97b817f5-0120-43d5-b9d8-8161e063ee87%40googlegroups.com> . For more options, visit https://groups.google.com/**grou**ps/opt_out<https://groups.google.com/groups/opt_out> .--
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Silvia Crivelli
Feb 14, 2014, 8:26:21 PM2/14/14
to diy...@googlegroups.com, cathal...@cathalgarvey.me
I'm sorry you had to go through all this trouble. Please send me email if you have any questions about ProteinShop. We no longer maintain it but will be happy to help.
-Silvia
On Friday, September 20, 2013 3:41:23 PM UTC-7, Cathal Garvey wrote:
On Friday, September 20, 2013 3:41:23 PM UTC-7, Cathal Garvey wrote:
Awesome stuff, thanks Tim! :)
On Fri, 20 Sep 2013 11:45:05 -1000
William Heath <wgh...@gmail.com> wrote:
> Hi Meredith,
>
> I am importing into github now.
>
> -Tim
>
> P.S.
>
> The repository will be located here:
>
> https://github.com/wheath/protein-shop
>
>
> On Fri, Sep 20, 2013 at 11:37 AM, Meredith L. Patterson
> <clon...@gmail.com
> > wrote:
>
> > Let's get it into github to start with. Tim, do you know how to do
> > that? If not, mail me a tarball of your source offlist?
> >
> > Cheers,
> > --mlp
> >
> >
> > On Fri, Sep 20, 2013 at 10:37 PM, Josiah Zayner
> > <josiah...@gmail.com>wrote:
> >
> >> Tim we appreciate your help but it would be much easier if you just
> >> posted a diff of the code you changed so it doesn't require
> >> someone using a virtual box to run the program. And we can test if
> >> it works on different platforms. If you can just run the diff
> >> commands against the original and new GLLineIlluminator.cpp file
> >> that would be very helpful.
> >>
> >> Thanks.
> >>
> >>
> >> On Fri, Sep 20, 2013 at 3:30 PM, William Heath <wgh...@gmail.com>
> >> wrote:
> >>
> >>> Hi All,
> >>>
> >>> I don't know why I am not making myself clear. I DID GET PROTEIN
> >>> SHOP TO COMPILE AND WORK!!!! Please download the oracle virtual
> >>> box appliance right here!!!
> >>>
> >>> http://www.graysonconsulting.biz/CentOS-6.4-i386-Gnome.ova
> >>>
> >>> Go to www.graysonconsulting.biz to see the login info and other
> >>> information you will need. Please stop making this harder than
> >>> it is. When you boot up the oracle virtual box image it will go
> >>> directly into protein shop loading ubiquitin!!! Can someone just
> >>> do this once so I can feel sane and that someone somewhere
> >>> understands what I did and why it is good pretty please?
> >>>
> >>> -Tim
> >>>
> >>> P.S.
> >>>
> >>> Meredith I would like to put this in github any help doing that is
> >>> appreciated. I don't know why it segfaulted on a different
> >>> protein other than ubiquitin but it did. One of my major goals
> >>> is 3d design with dna where the cell grows into a particular
> >>> shape, with particular cells of my design. I know it involves
> >>> hedgehog genes etc... Just like we give a model to a 3d printer,
> >>> I want to give a model to a program and have it output the dna
> >>> necessary to grow the 3d model. Any ideas on the best way to do
> >>> that? I have been told there are gaps in biological embriology
> >>> knowledge that doesn't make this feasible. My idea is to make
> >>> assumptions and fill in the gaps as knowledge increases but at
> >>> the same time discovering small experiments to try to test
> >>> theories. My idea is to use the zebra fish
> >>> (http://www.youtube.com/watch?v=wJNRIDWjX-o) for my growing
> >>> platform as it has a transparent egg to watch things growing. I
> >>> know protein cascade diffusion trigger cells to grow and change
> >>> etc... My idea is to use differential equations of diffusion
> >>> along with biobricks to sense proteins to cause the zebra fish
> >>> egg to grow in the desired way. Let me know your ideas.
> >>>
> >>>
> >>> On Fri, Sep 20, 2013 at 9:23 AM, John Dohnal
> >>> <johnh...@aol.com>wrote:
> >>>
> >>>> Hey whg,
> >>>>
> >>>> Wow, you people really know how to plow some hard soil! Didn't
> >>>> understand any of it, but GO TEAM DIYBIO!
> >>>>
> >>>> If its as buggy as you all say it is, I may be better off going
> >>>> with the other software recommendations, but if y'all can get it
> >>>> to run, I'll be in your debt!
> >>>>
> >>>> Thanks,
> >>>> John
> >>>>
> >>>>
> >>>> On Thursday, September 19, 2013 10:29:04 PM UTC-4,
> >>>> wgh...@gmail.comwrote:
> >>>>
> >>>>> It loaded!!!
> >>>>>
> >>>>> Check it out:
> >>>>>
> >>>>> http://imagebin.org/271405
> >>>>>
> >>>>>
> >>>>> On Thu, Sep 19, 2013 at 4:23 PM, Josiah Zayner
> >>>>> <josiah...@gmail.com>wrote:
> >>>>>
> >>>>>> ubiquitin probably the simplest structure you can find
> >>>>>> http://www.rcsb.org/pdb/**explore.do?structureId=1UBQ<http://www.rcsb.org/pdb/explore.do?structureId=1UBQ>
> >>>>>>
> >>>>>>
> >>>>>> On Thu, Sep 19, 2013 at 9:20 PM, William Heath
> >>>>>> <wgh...@gmail.com>wrote:
> >>>>>>
> >>>>>>> Hi All,
> >>>>>>>
> >>>>>>> It segfaulted reading the pdb. Here is the output:
> >>>>>>>
> >>>>>>> http://pastebin.com/k8ciJnzy
> >>>>>>>
> >>>>>>> Is there another simpler pdb it could read you think?
> >>>>>>>
> >>>>>>> -Tim
> >>>>>>>
> >>>>>>> P.S.
> >>>>>>>
> >>>>>>> I just removed all code from void
> >>>>>>> GLLineIlluminator::**enableLighting(GLContextData&
> >>>>>>> contextData) const to get it to compile. I will fix that
> >>>>>>> later, just want to see what is possible.
> >>>>>>>
> >>>>>>>
> >>>>>>> On Thu, Sep 19, 2013 at 4:10 PM, Josiah Zayner
> >>>>>>> <josiah...@gmail.com>wrote:
> >>>>>>>
> >>>>>>>> www.rcsb.org
> >>>>>>>>
> >>>>>>>> What did you do?
> >>>>>>>>
> >>>>>>>>
> >>>>>>>> On Thu, Sep 19, 2013 at 9:08 PM, William Heath
> >>>>>>>> <wgh...@gmail.com>wrote:
> >>>>>>>>
> >>>>>>>>> Hi All,
> >>>>>>>>>
> >>>>>>>>> I got it to compile! Here is a screenshot of it running:
> >>>>>>>>>
> >>>>>>>>> http://imagebin.org/271404
> >>>>>>>>>
> >>>>>>>>> Where can I get a pdb file or .pred file to test that it
> >>>>>>>>> works?
> >>>>>>>>>
> >>>>>>>>> -Tim
> >>>>>>>>>
> >>>>>>>>>
> >>>>>>>>> On Thu, Sep 19, 2013 at 3:59 PM, Josiah Zayner <
> >>>>>>>>> josiah...@gmail.com> wrote:
> >>>>>>>>>
> >>>>>>>>>> The code appears broke beyond brokenness. The website is
> >>>>>>>>>> down
> >>>>>>>>>> I would try emaling Sylvia at SNCrivelli [at] lbl.gov if
> >>>>>>>>>> you really want to try and get it working. However.
> >>>>>>>>>>
> >>>>>>>>>> If you want to do similar stuff I would install VMD
> >>>>>>>>>> or pymol: sudo apt-get install pymol
> >>>>>>>>>>
> >>>>>>>>>> for secondary structure prediction try PSIPRED:
> >>>>>>>>>>
> >>>>>>>>>> And for protein structure prediction use:
> >>>>>>>>>> http://swissmodel.expasy.**org/
> >>>>>>>>>> <http://swissmodel.expasy.org/> if it has some homology to
> >>>>>>>>>> some other structure
> >>>>>>>>>>
> >>>>>>>>>> or
> >>>>>>>>>> http://godzilla.uchicago.**edu/cgi-bin/aashish2/TerItFix/**
> >>>>>>>>>> TerItFix.cgi<http://godzilla.uchicago.edu/cgi-bin/aashish2/TerItFix/TerItFix.cgi>
> >>>>>>>>>> if it does not have any homology
> >>>>>>>>>>
> >>>>>>>>>> for Molecular Dynamics Simulations try namd which comes
> >>>>>>>>>> with VMD or gromacs: sudo apt-get install gromacs
> >>>>>>>>>>
> >>>>>>>>>>
> >>>>>>>>>>
> >>>>>>>>>> On Thursday, September 19, 2013 7:46:59 AM UTC-5, John
> >>>>>>>>>> Dohnal wrote:
> >>>>>>>>>>>
> >>>>>>>>>>> I have never used a Linux OS before, but I downloaded the
> >>>>>>>>>>> latest version of Ubuntu in order to run Protein Shop. I
> >>>>>>>>>>> downloaded the latest version of Protein Shop, but I
> >>>>>>>>>>> don't know how to start it. I know nothing about using
> >>>>>>>>>>> Linux, so any explicit, basic instructions would be most
> >>>>>>>>>>> helpful. In the readme file, it mentions some other
> >>>>>>>>>>> files that may need to be installed, but I don't even
> >>>>>>>>>>> know where to begin. Please help!
> >>>>>>>>>>>
> >>>>>>>>>>> Thanks,
> >>>>>>>>>>> John
> >>>>>>>>>>>
> >>>>>>>>>> --
> >>>>>>>>>> -- You received this message because you are subscribed to
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> >>>>>>>>>>
> >>>>>>>>>> Learn more at www.diybio.org
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> >>>>>>>>>> .
> >>>>>>>>>>
> >>>>>>>>>> For more options, visit https://groups.google.com/**
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> >>>>>>>>>>
> >>>>>>>>>
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Reason
Feb 16, 2014, 11:35:15 AM2/16/14
to diy...@googlegroups.com
On 02/14/2014 07:26 PM, Silvia Crivelli
wrote:
I'm sorry you had to go through all this trouble. Please send me email if you have any questions about ProteinShop. We no longer maintain it but will be happy to help.
It works for me with CentOS 6.4, but I never did get it to work in
Ubuntu 12.04 - it builds but doesn't otherwise function.
There are setup notes here:
https://github.com/exratione/protein-shop-vagrant
If you have a working modern Debian-style distro recipe, that would be appreciated.
---------------
Changes have been made to the ProteinShop Makefile: I switched to using gfortran rather than g77.
Dependencies on Ubuntu:
sudo apt-get install gfortran binutils-gold freeglut3-dev libfltk1.3-dev fluid
---------------
Reason
There are setup notes here:
https://github.com/exratione/protein-shop-vagrant
If you have a working modern Debian-style distro recipe, that would be appreciated.
---------------
Changes have been made to the ProteinShop Makefile: I switched to using gfortran rather than g77.
Dependencies on Ubuntu:
sudo apt-get install gfortran binutils-gold freeglut3-dev libfltk1.3-dev fluid
---------------
Reason
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