[Chimera-users] chimera visualization

Elaine Meng meng at cgl.ucsf.edu
Wed Sep 2 09:29:49 PDT 2015


Dear Valerio,
It should not matter, each is still a separate model.  If you open the PDB as model #0 but it contains an NMR ensemble, the members are models #0.1, #0.2, … etc.

I don’t know what steps you are using, but you can control exactly which structure(s) in which to show a particular residue in several ways.  Here are just two ways:

Ctrl-click to select the ribbon segment of just one residue in one structure (this mainly works for where they are not too close together), menu: Actions… Atoms/Bonds… show

Use a command, for example to show residue 45 of chain A in the 5th ensemble member of model 0 only:

display #0.5:45.A

You can use the balloon information that pops up when you hold the mouse cursor over some part a of a structure to tell you which model number and which residue it is.

Again, it is just the same as if you have multiple non-NMR structures open.
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 Sep 2, 2015, at 1:04 AM, Valerio Chiarini <valerio.chiarini at helsinki.fi> wrote:

> 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.
> Valerio
> 
> 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
> 




More information about the Chimera-users mailing list