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User:Wayne Decatur/3kg2 Morph Methods
From Proteopedia
First split all chains A, B, C, and D into single files and then used PyMol to change all chains to A for chains:
for example:
alter (chain B),chain='A'
sort
Used Beta server - mainly because it allows turning off fitting so I can show relationship of identical conformations, left fitting on for showing difference between chain A and chain B.
Next I was trying to get the subunit A to B morph to load already close to the familiar arrangement, so I tried in PyMol to orient it like I wanted it and then save all states (just fyi...found I could show all states at same time on screen with 'set all_states,1' from - PyMol reference card).
From http://www.mail-archive.com/pymol-users@lists.sourceforge.net/msg02004.html
found this series of commands (ENTERED ONE LINE AT A TIME) helped make a file with all models from PyMOL:
split_states 3kg2atob
delete 3kg2atob
alter all, segi = model[-4:]
rewind
save test.pdb, all
However, this didn't save the orientation I had moved it to at the start.
