On Dec 20, 2013, at 1:58 AM, Tetsuro Fujisawa wrote:

Hi,

I found some strange behavior in saving pdb file by script file.
I tried to modify the orientation of pdb file ‘tst.pdb’ (#1) in reference to axis coordinate (#0), then save the atomic coordinates in pdb file.
When I typed in the commands through either command line window or IDLE, transformed coordinates were saved. It worked fine. However, the exact identical commands (inside the brancket) or lines (rc(’..’)) were run by script file shown in below, the untransformed coordinates were saved.  This is also the case for “Midas.write method”.  
I wondered this might be a bug.

Regards,
Tetsuro

Sample.py:
----------------------------------------------
from chimera import runCommand as rc

rc('open axis.bild')
rc('open tst.pdb')
rc('rock y 60 1 center #1 coord #0 models #1')
# orientation of tst.pdb was modified
rc('focus')
rc('write relative #0 #1 tstA.pdb')
# write current coordinates to tstA.pdb
rc('open tstA.pdb')
# opened tstA has original untransformed orientation
-----------------------------------------------


Hi Tetsuro,
The issue is that unlike using the command line or IDLE or running a chimera-command script, no frames get drawn during the execution of a Python script unless explicitly requested and therefore the "rock" command in your script doesn't actually do anything until after the entire script runs, and by that time your coordinate file has already been written.
To get the rock command to complete before proceeding with the rest of the script you need to append "; wait" or "; wait 1" (since you are rocking for 1 frame) to the end of your rock command.


--Eric

                        Eric Pettersen

                        UCSF Computer Graphics Lab

                        http://www.cgl.ucsf.edu