[Chimera-users] saving pdb with transformed coordinates

Michael Elbaum michael.elbaum at weizmann.ac.il
Thu Dec 1 13:42:04 PST 2016

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 :-)

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 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.


I hope this helps,
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,

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