[Chimera-users] Driving matchAtoms from the IDLE

[Jean-Didier Maréchal]

Hi Guys,

I'd like to superpose two inorganic complexes using two differently
"ordered" atom sets. My compound has quite similar substructures but I
am  sure at all what is the best "ordered" selection of atom pairs to
align. Therefore, I'd like to make a "extensive" search (with an
heuristic approach to define...) passing by the idle. I am unfortunately
missing something before getting to this point! 

Lets say that I just want to align the nitrogen atoms of the my two
structures. I have:

import chimera
import numpy
from chimera import match
from chimera import runCommand
runCommand("select #1 at N=")
an1=chimera.selection.currentAtoms()
runCommand("select #0 at N=)
an2=chimera.selection.currentAtoms()
chimera.match.matchAtoms(an1,an2)

And then it's when I am already stuck! 

the resulting prompt does not provide mistake an gives:
chimera.match.matchAtoms(an1,an2)
(<_chimera.Xform object at 0x9463ef8>, 0.034256915079603358)

But how this results can be send to the graphical window? I guess I have
to use the Xform object, but I can not clearly understand how to do
this.

Thanks for any help!

JD


On Thu, 2008-02-21 at 12:00 -0800, chimera-users-request at cgl.ucsf.edu
wrote:
> Send Chimera-users mailing list submissions to
> 	chimera-users at cgl.ucsf.edu
> 
> To subscribe or unsubscribe via the World Wide Web, visit
> 	http://www.cgl.ucsf.edu/mailman/listinfo/chimera-users
> or, via email, send a message with subject or body 'help' to
> 	chimera-users-request at cgl.ucsf.edu
> 
> You can reach the person managing the list at
> 	chimera-users-owner at cgl.ucsf.edu
> 
> When replying, please edit your Subject line so it is more specific
> than "Re: Contents of Chimera-users digest..."
> 
> 
> Today's Topics:
> 
>    1. Re: distance (Elaine Meng)
> 
> 
> ----------------------------------------------------------------------
> 
> Message: 1
> Date: Thu, 21 Feb 2008 09:00:37 -0800
> From: Elaine Meng <meng at cgl.ucsf.edu>
> Subject: Re: [Chimera-users] distance
> To: "??" <lynnwuchao at gmail.com>
> Cc: chimera-users at cgl.ucsf.edu
> Message-ID: <0E85C396-8C7D-4182-A029-5C0155245C3A at cgl.ucsf.edu>
> Content-Type: text/plain; charset=UTF-8; delsp=yes; format=flowed
> 
> Hi!
> 
> The distances are listed in a separate dialog - choose "Tools...  
> Structure Analysis... Distances" from the menu to open that dialog.   
> You can adjust the number of decimal places in the measurement, and  
> there is a "Save" button if you want to save distances or other  
> measurements to a text file.
> 
> I hope this helps,
> Elaine
> -----
> Elaine C. Meng, Ph.D.                          meng at cgl.ucsf.edu
> UCSF Computer Graphics Lab and Babbitt Lab
> Department of Pharmaceutical Chemistry
> University of California, San Francisco
>                       http://www.cgl.ucsf.edu/home/meng/index.html
> 
> 
> 
> 
> On Feb 20, 2008, at 11:38 PM, ?? wrote:
> 
> > Hi, folks,
> > I select two atoms and measured their distance using the command  
> > distance and can see the exact distance value in the graphic  
> > interface, but when I go the log file i can not find it.
> > Can anybody give me a hand  and tell me why can I find it? Thanks..
> > _______________________________________________
> > Chimera-users mailing list
> > Chimera-users at cgl.ucsf.edu
> > http://www.cgl.ucsf.edu/mailman/listinfo/chimera-users
> 
> 
> 
> ------------------------------
> 
> _______________________________________________
> Chimera-users mailing list
> Chimera-users at cgl.ucsf.edu
> http://www.cgl.ucsf.edu/mailman/listinfo/chimera-users
> 
> 
> End of Chimera-users Digest, Vol 58, Issue 24
> *********************************************