[Chimera-users] How to get central cross section which pass through two asigned cross axis

Jian Guan jug25 at psu.edu
Fri Dec 27 10:50:19 PST 2013

Dear all,
I have a density map of virus-Fab complex. I want to make a central cross
section which pass through the Fab pseudo-symmetry 2-fold axis. I have
measure the angle of Fab relative to the capsid. 
Hope someone can help me.
Thank you so much.
Sincerely yours,

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Subject: Chimera-users Digest, Vol 128, Issue 25

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Today's Topics:

   1. Re: saving coords from script (Eric Pettersen)


Message: 1
Date: Mon, 23 Dec 2013 15:59:16 -0800
From: Eric Pettersen <pett at cgl.ucsf.edu>
To: Tetsuro Fujisawa <fujisawa at gifu-u.ac.jp>
Cc: "chimera-users at cgl.ucsf.edu Mailing List"
	<chimera-users at cgl.ucsf.edu>
Subject: Re: [Chimera-users] saving coords from script
Message-ID: <04B15E0C-844B-4594-8AE6-760588744D85 at cgl.ucsf.edu>
Content-Type: text/plain; charset="windows-1252"

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 Pettersen
                        UCSF Computer Graphics Lab

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