[Chimera-users] saving pdb with transformed coordinates

Elaine Meng meng at cgl.ucsf.edu
Thu Dec 1 13:04:25 PST 2016


Hi Michael,
I was unable to reproduce this problem… I tried “turn y 90”  and then "write #0 ~/Desktop/test.pdb” and it did write the transformed coordinates, and should behave the same way if run via python with rc.  I guess you can doublecheck  by actually typing commands (let us know if still problematic) and then make sure the same commands are used in your script.

A separate issue:  I see your script uses “rock” whereas you probably wanted “roll” or “turn” … note that “rock y 10 1” will not rotate 10 degrees, but perform 1 frame of a rocking oscillation that would have covered a 10 X 20 = 200-degree angle had it been allowed to perform a full cycle of 136 frames.  Instead use “turn y 10”  or “roll y 10 1” if you want to rotate 10 degrees around Y.

<http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/rock.html>
<http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/turn.html>

I hope this helps,
Elaine
-----
Elaine C. Meng, Ph.D.                       
UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab
Department of Pharmaceutical Chemistry
University of California, San Francisco

On Dec 1, 2016, at 10:23 AM, Michael Elbaum <michael.elbaum at weizmann.ac.il> wrote:

> Dear Chimera people,
> 
> I'm trying to create a series of pdb files showing a single structure rotated around a given axis. Using the GUI I can turn the molecule and save the pdb after unclicking the "Use untransformed coordinates" box. However, when I run a script using the write command I don't know how to invoke this option. The docs on the "relative" option suggest that the default is to write transformed coordinates.
> 
> I've tried the following:
> for i in xrange(0,90,10):
>     rc("rock " + "y " + str(i) + " 1")
>     fn = basefn + str(i) + '.pdb'
>     rc("write format pdb 0 " + fn)
> and the files end up identical although the rotation around y does appear on the screen. I had the problem in version 1.10.2 and it remains after upgrading to 1.11.
> 
> thanks for your help,
> Michael




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