[Chimera-users] Overlay structures in Chimera (UNCLASSIFIED)

Elaine Meng meng at cgl.ucsf.edu
Tue Jan 28 10:05:29 PST 2014


On Jan 28, 2014, at 9:45 AM, "Keasey, Sarah L CTR USARMY MEDCOM USAMRIID (US)" <sarah.l.keasey.ctr at mail.mil> wrote:

> Elaine,
> 
> I have a new question regarding overlaying structures using Chimera.
> 
> I have opened two structures in Chimera. I am trying to move them so that they are overlaid. It appears as though I should be able to inactivate one of the structures in order to freely move the other, but this doesn't work for me and I'm not sure where I am going wrong. When I inactivate one structure, I can freely rotate the other, but not move it from one place to another. I have watched the youtube video here: http://www.youtube.com/watch?v=6VGYo1pRRZ8 which deals with merging two structures, and also watched the "Sequential Fitting" video on the "Videos" page of the UCSF Chimera site.
> 
> Any suggestions for what I am doing wrong? I apologize for such elementary questions, I am a new Chimera user.
> 
> Thanks in advance,
> Sarah Keasey

Hi Sarah,
(we generally ask everyone to send questions to chimera-users at cgl.ucsf.edu, CC'd here, so that everybody can benefit, unless the data are private)

Those videos aren't that relevant to your situation.  More relevant is the manual page discussing the various ways to superimpose structures.   The Chimera User's Guide can be searched or browsed from the Help menu, or you can see the same thing on our website, e.g.:
<http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/superposition.html>

If using the mouse to move one structure, what you did is exactly correct: inactivate the other structure.   The mouse should continue to work exactly the same for the movable structure as when everything was movable (both rotation and translation).   The default control for XY-translation is middle mouse button, if you have one.  For touchpad or mouse with fewer buttons, see here:
<http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/mouse.html>

However, more often one doesn't use the tedious approach of trying to do it by hand, and instead uses one of the other superposition methods.  The easiest is usually MatchMaker (in the menu under Tools… Structure Comparison), so I would try that first.
<http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/matchmaker/matchmaker.html>

To help you become more familiar with Chimera, there are several tutorials in the User's Guide (again also available from Help menu), ranging from "getting started" to more advanced.
<http://www.rbvi.ucsf.edu/chimera/current/docs/UsersGuide/frametut.html>

I hope this helps,
Elaine
----------
Elaine C. Meng, Ph.D. 
UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab
Department of Pharmaceutical Chemistry
University of California, San Francisco




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