User:Wayne Decatur/3kg2 Morph Methods: Difference between revisions
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First split all chains A, B, C, and D into single files and then used PyMol to change all chains to A for chains:<br> | First split all chains A, B, C, and D into single files and then used PyMol to change all chains to A for chains:<br> | ||
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for example:<br> | for example:<br> | ||
alter (chain B),chain='A' <br> | alter (chain B),chain='A' <br> | ||
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Used [http://molmovdb.org/cgi-bin/beta.cgi 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. | Used [http://molmovdb.org/cgi-bin/beta.cgi 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 rotate it and 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:<br> | |||
<br> | |||
split_states 3kg2atob | |||
delete 3kg2atob | |||
alter all, segi = model[-4:] | |||
rewind | |||
save test.pdb, all | |||
