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.h...
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/matchmak...
<http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/multalignviewer/mul...
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@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