[Chimera-users] Driving matchAtoms from the IDLE
jeandidier.marechal at uab.es
Fri Feb 22 03:45:11 PST 2008
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:
from chimera import match
from chimera import runCommand
runCommand("select #1 at N=")
runCommand("select #0 at N=)
And then it's when I am already stuck!
the resulting prompt does not provide mistake an gives:
(<_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
Thanks for any help!
On Thu, 2008-02-21 at 12:00 -0800, chimera-users-request at cgl.ucsf.edu
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> 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
> 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 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
> 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..
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