problems with e2boxer in windows?

[Michael Landsberg]

Hi,

 

Just wondering if anyone else has experienced problems with boxing out particles in eman2 under windows7?  I am running the e2workflow gui and have picked particles, but when I try to generate output I seem to be getting nowhere.

 

My list of raw data files indicates varying numbers of “stored boxes” next to each micrograph but “particles on disk” is just 0 (i.e. a “-“).  When I select the files and hit OK as instructed, the window closes, sending me back to e2workflow, and it appears as though nothing has happened. 

 

Hopefully I am just overlooking something obvious?

 

 

--

Dr Michael J Landsberg
Senior Research Officer
Division of Chemistry and Structural Biology
Institute for Molecular Bioscience
The University of Queensland
St Lucia, Qld, 4072
AUSTRALIA

Phone: +61 7 3346 2010
E-mail: m.lan...@uq.edu.au

Skype: michael.landsberg

 

Register now for the East Coast Protein Meeting 2011

http://compbio.biosci.uq.edu.au/QPG/ECPM11

 

[Tang, Guang]

Is there a permission issue for the directory you write to?

Grant
________________________________________
From: em...@googlegroups.com [em...@googlegroups.com] On Behalf Of Michael Landsberg [m.lan...@imb.uq.edu.au]
Sent: Tuesday, November 08, 2011 8:02 PM
To: em...@googlegroups.com
Subject: [EMAN2] problems with e2boxer in windows?

Hi,

Just wondering if anyone else has experienced problems with boxing out particles in eman2 under windows7? I am running the e2workflow gui and have picked particles, but when I try to generate output I seem to be getting nowhere.

My list of raw data files indicates varying numbers of “stored boxes” next to each micrograph but “particles on disk” is just 0 (i.e. a “-“). When I select the files and hit OK as instructed, the window closes, sending me back to e2workflow, and it appears as though nothing has happened.

Hopefully I am just overlooking something obvious?

--
Dr Michael J Landsberg
Senior Research Officer
Division of Chemistry and Structural Biology
Institute for Molecular Bioscience
The University of Queensland
St Lucia, Qld, 4072
AUSTRALIA

Phone: +61 7 3346 2010

E-mail: m.lan...@uq.edu.au<mailto:m.lan...@uq.edu.au>
Skype: michael.landsberg

Register now for the East Coast Protein Meeting 2011

http://compbio.biosci.uq.edu.au/QPG/ECPM11<http://compbio.biosci.uq.edu.au/QPG/ECPM11/index.html>

--
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[Michael Landsberg]

I suspected this. However, the source (micrograph) files are located in a subfolder of "my documents" and it seems as though EMAN2 is writing the output to the desktop of my user area though (not an administrator account). There is an EMAN2DB folder and a particles folder that contains an EMAN2DB subfolder populated with a _ptcls.bdb and a _ptcls_256x256x1 file for each micrograph located on my desktop along with shortcuts to the various e2 programs (display/workflow/py).

[Michael Landsberg]

FYI: I tried changing the working dir and it seems to be OK now. May have been a permissions problem, may have been a memory problem also.

Thanks for your help!

[Michael Landsberg]

As a follow up to the problem below, I am running into further problems with eman2 in windows 7.

Boxing now works fine from the workflow. I get stuck though when I try to combine boxed out particles into a dataset using the build particle sets command in e2workflow I run into problems. I get a python dialog box coming up with "making virtual stacks" and a progress bar. The process seems to halt though at a variable percentage value (usually around 60-70%), but which is always the same if I choose the same subset of particles. It seems to freeze once it gets to a total dataset of maybe >150 particles (or thereabouts) which is pretty limiting for further analysis.

One additional thing I have noticed is that nothing ever seems to appear in the "running processes" window.

I have just recently installed e2.04 but the problem persists.

The fact that this seems to occur at a certain dataset size makes me think that maybe it is tied to system performance, so I have detailed my specs below - should I expect any problems with this system?

64 bit Windows 7 enterprise (service pack 1)
Intel Core i5-2520M 2.5GHz
4Gb RAM
System rating (windows experience index) = 4.9
- 7.1 calculations per sec
- 7.2 memory ops per sec
- 4.9 Desktop graphics performance for windows Aero
- 6.4 3D business and gaming graphics performance
- 5.9 Disk data transfer rate

[Steven Ludtke]

Hi Michael. As always, windows remains our least well-tested platform (and there are some good reasons
for this). Nonetheless, everything you're doing should be fine. A couple of other questions:

- What box size are you using ?
- e2bdb.py particles -l
- e2bdb.py sets -l
if either of those two commands lock up, then something is going on with your database files. If they both
work, we'll have to think more...

----------------------------------------------------------------------------
Steven Ludtke, Ph.D.
Associate Professor, Dept. of Biochemistry and Mol. Biol. Those who do
Co-Director National Center For Macromolecular Imaging ARE
Baylor College of Medicine The converse
slu...@bcm.edu -or- ste...@alumni.caltech.edu also applies
http://ncmi.bcm.edu/~stevel

[Michael Landsberg]

Hi Steve,

Box size is 256x256x1

Both commands seem to work fine.

[Ludtke Steven]

Ok, I think Grant is going to have to look into this with you...