[Chimera-users] Mutations or residue selections

Elaine Meng meng at cgl.ucsf.edu
Mon Oct 13 16:19:11 PDT 2014


Dear Susan,
Of course you can hide/show any parts of the ribbon and atoms/bonds  in the structure that you want.  See menu Actions… Atoms/Bonds… hide/show, and Actions… Ribbons… hide/show.  You specify the parts you want to act on using the menu by “selection,” see:
<http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/selection.html>

Or, you can do it with commands, e.g. “display” and “~display” for atoms/bonds and “ribbon” and “~ribbon” for hiding and showing ribbons.  In that case, you specify the parts you want to act on with the command using command-line specification, see:
<http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/frameatom_spec.html>

For example:
   ~ribbon
   ribbon :100-200.A,200-260.A

For becoming familiar with these basic paradigms of Chimera, you may want to take a look at the “getting started” tutorial on our website:
<http://www.rbvi.ucsf.edu/Outreach/Tutorials/GettingStarted.html>
…. and/or the tutorials in the User’s Guide, which you can open from the Chimera Help menu (especially the getting started and image ones).

You can only do a simple first-order analysis of a mutation by looking at whether the swapped sidechain clashes with other atoms or loses favorable interactions such as H-bonds, assuming the rest of the protein stays in place.  Chimera does not predict the resulting overall complicated conformational change that might occur, or changes in free energy of folding, etc.  The simple virtual mutation can be done with the Rotamers tool (in menu under Tools… Structure Editing) or “swapaa” command.  Click the Help button on the Rotamers tool or use command “help swapaa” for details.  There is some example usage of Rotamers in the Structure Analysis and Comparison tutorial in the User’s Guide.

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

On Oct 13, 2014, at 12:41 PM, Susan Cotmore <susan.cotmore at yale.edu> wrote:

> Hi,
>        Is it possible to set up structures in Chimera so that only segments of an amino acid chain are visible, eg residues 100-200 and 220-260 in a 300 residue chain?
> 
>        Is it possible to model potential effects of introducing specific mutations?
> Many thanks,
> Susan Cotmore




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