[Chimera-users] saving pdb with transformed coordinates

[Michael Elbaum]

Thanks Elaine and Erik!      I changed to turn but the wait step was the key. It seems the writing got out of sync with the transform otherwise. working now :-)
regards,
Michael

________________________________
From: Eric Pettersen [pett at cgl.ucsf.edu]
Sent: Thursday, December 01, 2016 23:12
To: chimera-users at cgl.ucsf.edu BB
Cc: Michael Elbaum
Subject: Re: [Chimera-users] saving pdb with transformed coordinates

Elaine’s response caused me to realize the other problem with your script — you are going to need to add “; wait” to the end of any rock/roll/turn command you use.  Otherwise the script will keep going without any frames being drawn, which also means that no motion from the rock/roll/turn will have occurred, and therefore the coordinates will be unchanged when the script reaches your “write” command.

—Eric

Eric Pettersen
UCSF Computer Graphics Lab

On Dec 1, 2016, at 1:04 PM, Elaine Meng <meng at cgl.ucsf.edu<mailto:meng at cgl.ucsf.edu>> wrote:

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<mailto: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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