Euler angle modification

[Marjolaine]

Hi,

I am working with Michèle Auger at Laval University. We are looking at
membrane-peptide interactions using oriented sample on glass plates.
In order to simulate different organisation, we would like to modified
the angle distribution. Some publications used the therm "shape
factor" to describe this distribution of euler angle. Our question is:
how to created an eulerangle file? Can you send us an example so we
may modified it?

Thanks you for your help,
Marjolaine

[Mikhail Veshtort]

Hi Marjolaine,

Creating the file of orientations is very easy, as the format for
this file is just three or four columns (alpha beta weight, or
alpha beta gamma weight). The weights should add up to one.

In your situation, the most important thing is to have an appropriate
model for the distribution of orientations in your sample. But this
is not exactly trivial. Perhaps, you could take a highly uniform
sampling set (one of the REPULSION sets would work best here) and use
it with some model distribution of the weight, which should be given
as an explicit function of (alpha, beta). With this approach, you
will probably find that it is more convenient to use the euler_CR
matrix variable than an external orientations file.

Mikhail

[Marjolaine]

I want fist to tank you for this fast answer. We are considering the
two option you proposed.

Unfurtunately, we are still unable to generate the euler angle file.
We created a three columns file (name sphere.txt), as simple as:
0 90 0.5
0 0 0.5

change the euleur file name to:
EulerAngles sphere1.txt

but we still get an error message. We tried every thing we could think
of without any result.
It might be trivial, but still we don't know how to do it.

Thanks for your help,
Marjolaine

[Jonathan Helmus]

Marjolaine,

I believe all Euler angle files user values in radians (so 0 1.570796
0.5, etc ). For examples of both type of file see Malcolm Levitt's
collection of angle sets:
http://www.mhl.soton.ac.uk/public/Main/software/Orientations/index.html

--
-Jonathan Helmus

Chemical Physics Graduate Student
Ohio State University
http://www.chemistry.ohio-state.edu/~jhelmus/

[Mikhail Veshtort]

Hi Marjolaine,

What does the error say?

Mikhail

[Marjolaine]

The message is: Error found while reading file "sphere1.txt"

And I tried with radians without any results.
Marjolaine

[Marjolaine]

Can the problem be located in any file conversion from unix to dos or
vice versa ?
we run spinev under win XP... Thanks

Marjolaine

> > Mikhail- Masquer le texte des messages précédents -
>
> - Afficher le texte des messages précédents -

[Mikhail Veshtort]

Hi Marjolaine,

Is it possible that you use non-Unix line ending in your file? You
can check this by running
cat -v filename
in any unix shell. This should not show ^M or any other strange
characters.
If you work on a Windows PC, you should edit files with some Unix-
compliant text editor, like PSpad.

Mikhail

[Marjolaine]

I did convert the txt file with a dos2unix software, but the same
error occured...

Marjolaine

[Mikhail Veshtort]

Marjolaine,

Please send your files (as attachments) to my email address. I'll try
to reproduce the error.

Mikhail

[Mikhail Veshtort]

Hi Marjolaine,

As I suspected, the sphere1.txt file you sent me contains non-
standard characters, which spinev does not know how to interpret. To
avoid these problems, use PSPad editor (and choose Unix file format
there).

Best,
Mikhail

[Marjolaine]

Thanks!
Marjolaine