[Chimera-users] chimera help
meng at cgl.ucsf.edu
Thu Apr 2 09:41:21 PDT 2009
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.
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).
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).
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
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:
I hope this helps,
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
On Apr 1, 2009, at 3:34 PM, Terrance Chiang wrote:
> 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
> Any help would be highly appreciated!
> Terrance Chiang
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