[Chimera-users] Querie: Ligand superimposition

Elaine Meng meng at cgl.ucsf.edu
Fri Sep 6 10:08:49 PDT 2013


Hi Graziella,
Not sure I understand the question, but you can display/undisplay any atoms that you want (without deleting) or you could delete the atoms you don't want. There are certainly many different ways you could do it, but the specifics would depend on the details of your data.  First I'll mention showing/hiding and then superposition.

For example, you could hide the protein ribbons and atoms with commands:
~ribbon protein
~disp protein

... but there might still be other stuff you didn't want like water, so you would also have to hide those. These things could also be done with the menu instead of commands, but it would take more words to describe.

Or, you could select only the atoms you want to show, and then use commands:
sel invert
~ribbon sel
~disp sel

You also mentioned you wanted to superimpose the ligands. Here is a discussion of the different ways to superimpose structures in Chimera, with links to the relevant manual pages ... the "match" command may be appropriate for your ligands:
<http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/superposition.html>

To learn about more general features like displaying/undisplaying atoms and ribbons, you may want to try the "getting started" tutorial
<http://www.rbvi.ucsf.edu/Outreach/Tutorials/GettingStarted.html>

and take a look at command-line atom specification
<http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/frameatom_spec.html>

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

On Sep 6, 2013, at 5:26 AM, Graziella Portelli wrote:

> Dear Chimera Team
> 
> Hope this email finds you in good health.
> 
> I am using UCSF Chimeria for my de Novo drug design disseration.
> I am still learning the basic functions that this software offers, however have not been able to figure out the following.
> Basically I need to put into one picture/frame the original ligand or my receptor and the possible ligands (generated by Ligbuilder). They have the same general structure with some changes and I need to superimpose them, but show them at separate levels. Is this possible to do this for only the ligands and not the receptor protein? 
> 
> I eagerly await your reply,
> 
> Graziella Portelli
> B.Pharm 




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