meng at cgl.ucsf.edu
Sat Mar 31 09:15:17 PDT 2012
First make sure you are hiding the input conformations, so that you are seeing only the morph (for example, you could show Model Panel from Favorites menu, then uncheck the S(hown) boxes for everything except the morph results). I say that because if you see something not moving, it might be the original structure.
As explained here, the morph should contain all of the atoms in the protein chain that are included in all of the input structures.
Since your input structures are the same protein, if each one includes the sidechain atoms, the morph should contain all the same sidechains and they should move from one position to the other during the morph. They may not be displayed automatically, however. Try displaying all atoms (again better to hide the other structures first) to make sure of what is there.
About the ion: even if the ion is in both structures, it may not be in the morph if you are using an older version of Chimera. However, there have been some fixes, and I believe if you are using Chimera 1.6 or newer, the ion should be included. The fix I'm thinking of was 6 months ago and is described here:
If you try Chimera 1.6 and the suggestions above but you believe there is a bug, you could use Help... Report a Bug in the menu and describe how to reproduce the problem, attaching session file if necessary.
I hope this helps,
Elaine C. Meng, Ph.D.
UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab
Department of Pharmaceutical Chemistry
University of California, San Francisco
On Mar 31, 2012, at 5:24 AM, Francesco Malatesta wrote:
> Hello from Rome!
> I'm trying to morph 2 different conformations of the same protein. I get a very very nice movie, but I can't get amino acid side chains or heteroatoms (heme iron) to move also.
> Is there any way to do this?
> thank you for help
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