[Chimera-users] chimera help

[Elaine Meng]

Hi Terrance,
I'm not sure what you were trying.  You can just open the two  
structures and show them in any style you want, including molecular  
surfaces.  I am assuming you already have the two structures.  Chimera  
can "mutate" one amino acid to another, but other than choosing the  
best possible rotamer for the new amino acid, it will not predict  
structural changes caused by a mutation.
<http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/rotamers/framerot.html 
 >

If the structures are not already matched or superimposed, you can use  
MatchMaker to superimpose them, and if you use the MatchMaker option  
to show the sequence alignment, that will automatically show an RMSD  
histogram above the sequences (for 2 sequences, the bar height shows  
simply the CA-CA distance in each column).
<http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/matchmaker/matchmaker.html 
 >
<http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/multalignviewer/multalignviewer.html#headers 
 >

If you want the structures side by side rather than superimposed, you  
would first superimpose them and then translate one of them along the  
laboratory Y axis with the command "move" (or translate each one but  
in opposite directions, e.g. one to the left and one to the right).
<http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/move.html>

If you show surfaces (e.g. Actions... Surface... show) it is often too  
confusing to superimpose two structures, and the side-by-side approach  
may be better.  You can color the surfaces by properties such as  
hydrophobicity (see Presets... Interactive 3 (hydrophobicity surface))  
or Coulombic electrostatic potential (see Tools... Surface/Binding  
Analysis... Coulombic Surface Color -- for that you need a recent  
daily build).

If you need more details on any of these I can point you to the  
relevant manual pages.  There are also tutorials on structure analysis  
and comparison of related structures:
<http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/tutorials/ 
squalene.html>
<http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/tutorials/alignments.html 
 >

I hope this helps,
Elaine
-----
Elaine C. Meng, Ph.D.                          meng at cgl.ucsf.edu
UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab
Department of Pharmaceutical Chemistry
University of California, San Francisco
                      http://www.cgl.ucsf.edu/home/meng/index.html

On Apr 1, 2009, at 3:34 PM, Terrance Chiang wrote:

> Hi,
> I am trying to show a structural change between two proteins that  
> differ by one amino acid, is this possible with chimera?
>
> I was unable to display the transformation I desired, so I looked  
> into other ways to show changes between two overall similar  
> molecules. I found that it is possible to show a change in the  
> surface between two similar molecules, but I am unable to utilize  
> the function because it requires a different file format.
>
> I would like to do both... that is, to show the conformational  
> change from one protein to another, as well as show the change in  
> surface from one protein to another, but I keep hitting these road  
> blocks.
>
> Any help would be highly appreciated!
>
> Thanks,
> Terrance Chiang