[Chimera-users] How to explore two protein structures on the same screen?

Jing Tang jing.tang at helsinki.fi
Fri Jul 31 04:41:47 PDT 2015


Thanks Elaine. These links are very helpful.
Jing

-----Original Message-----
From: Elaine Meng [mailto:meng at cgl.ucsf.edu] 
Sent: 29. heinäkuuta 2015 20:21
To: Jing Tang
Cc: chimera-users at cgl.ucsf.edu
Subject: Re: [Chimera-users] How to explore two protein structures on the
same screen?

Hi Jing,
For an overview, you might want to try the “getting started” tutorial --
moving separately is mentioned in “models and model status,” and specifying
individual residues is covered in “selection with the mouse” and
“command/target”: 
<http://www.rbvi.ucsf.edu/Outreach/Tutorials/GettingStarted.html>

However, I’ll try to list the ways briefly in this message.

There are many ways to move structures separately:
(1) “freezing” (deactivating) some structure(s) and moving the others with
the mouse
<http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/mouse.html#activedef>
(2) superimposing similar structures
<http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/superposition.html>
(3) using movement commands (move, turn, etc.) with “models” keyword to move
only specific models
<http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/move.html>

There are many ways to act on individual residues:
(1) selecting them with Ctrl-click on the structure
<http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/selection.html#pickselect>
(2) selecting them in the sequence window (menu: Favorites
 Sequence)
<http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/multalignviewer/f
ramemav.html>
(3) just specifying the residue(s) directly in a command, for example:

color red #0:325.A

 to color residue 325 in chain A of model 0 select #1:45.A,55.B 
 to select
residues 45 in chain A and 55 in chain B of model 1
<http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/atom_spec.html#hiera
rchy>

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 Jul 28, 2015, at 1:29 AM, Jing Tang <jing.tang at helsinki.fi> wrote:

> Hi,
> I opened two protein structures, say 2JIT and 4WA9 and they were partially
overlapped on the screen. How to move one protein so that they can be
separated more? I can only move the two proteins as a whole but not
individually.
> Further, I would like to highlight one residue for a particular protein
and I could not find a way to first select a protein and then a residue. 
> Thanks,
> Jing





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