[Chimera-users] chimera visualization

Valerio Chiarini valerio.chiarini at helsinki.fi
Wed Sep 2 01:04:22 PDT 2015

Hi Elaine,

the problem is that the structures I superimpose with matchmaker  
belong to the same pdb file, which means that I can select one chain  
but when I am about to show a residue (eg. ser) in stick the previous  
selection disappears and the serines of all structures are shown.


Quoting Elaine Meng <meng at cgl.ucsf.edu>:

> Dear Valerio,
> It should be no problem.  Just superimpose the structures and show  
> their backbones as sticks, in the same way as for crystal structures.
> You could superimpose with MatchMaker (in menu under Tools…  
> Structure Comparison) or with Ensemble Match (in menu under Tools…  
> MD/Ensemble Analysis).
> <www.rbvi.ucsf.edu/chimera/docs/UsersGuide/superposition.html>
> There are examples of using these tools in various tutorials:
> <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/tutorials/alignments.html>
> <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/tutorials/ensembletut.html>
> You can show backbone sticks with the Actions menu or with commands,  
> for example:
> open 1g1p
> ~ribbon
> disp @n,ca,c,o
> 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 Aug 31, 2015, at 5:19 AM, Valerio Chiarini  
>> <valerio.chiarini at helsinki.fi> wrote:
>> Dear Elaine,
>> I would like to produce images from chimera showing an NMR bundle  
>> structure (backbone only) with stick-represented residues each one  
>> belonging to different single structures. I know it´s possible to  
>> do it with pymol but unfortunately the structures superimposition  
>> is not as good as in chimera. Would it be possible?
>> Thank you in advance,
>> Valerio

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