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@N=") an1=chimera.selection.currentAtoms() runCommand("select #0@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@cgl.ucsf.edu wrote:

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Today's Topics:

1. Re: distance (Elaine Meng)

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Message: 1 Date: Thu, 21 Feb 2008 09:00:37 -0800 From: Elaine Meng <meng@cgl.ucsf.edu> Subject: Re: [Chimera-users] distance To: "??" <lynnwuchao@gmail.com> Cc: chimera-users@cgl.ucsf.edu Message-ID: <0E85C396-8C7D-4182-A029-5C0155245C3A@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@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:

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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@cgl.ucsf.edu http://www.cgl.ucsf.edu/mailman/listinfo/chimera-users

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