I have two objects of the same protein in different conformational states and I want to show the conformational change using morph. Each object is a homopentamer, chains A-E. However, one object has the chains arranged in a clockwise direction and the second object has them arranged in a counterclockwise direction. When I morph them, I get a wierd twisty thing as a result of chains swapping with one another. I tried to fix this by changing the names of the chains (alter PDB1 and chain B, chain="E" ...and so on) so that now chain names A-E of both PDBs are clockwise. Although I succeed in renaming the chains, this has has no effect on the morphing. SO, I wondered if the segment identifer was the problem. Each chain also has a corresponding segment identifier (for example, originally PDB1/B/B which has now been changed to PDB1/B/E). I tried changing the segment identifier using the same syntax (alter PDB1 and segment B, segment="E"). Although the output message shows "modified 2667 atoms" the segment identifier in the sequencce window does not change and selection of segment E yields nothing and the morphing is unchanged. Sorry for the long narrative, but the main question is: what can I do to make this morphing work? Thanks.
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