Hi Ryan,
ChimeraX has a "morph" command. Here's an example using it
open 2vaa open 2vab matchmaker #2 to #1 morph #1,2 save morph.pdb model #3 allCoordsets true
Morphing of course only contains the atoms that are in both structures. So if you have an unbound and a bound state, and the bound tapasin is only in one structure then it will not be included in the morph since there is nothing to morph it to in the unbound state. You can delete chains that the two structures do not have in common before morphing, or you can use the same true option to the morph command "morph #1,2 same true" which will ignore chains which do not appear in both structures.
Tom
On Apr 29, 2022, at 9:28 AM, Kissinger, Ryan (NIH/NIAID) [C] ryan.kissinger@nih.gov wrote:
Hi Tom,
I’m trying to create a morph animation in ChimeraX and I am having a lot of trouble finding decent tutorials online. I have pdb entries for unbound MHC1 and Tapasin and bound MHC1 and Tapasin. If possible I would like to morph between the bound and unbound forms. I would like to do this with ribbon and the atomic models. Any advice?
Best Regards,
Ryan