User:Wayne Decatur/3kg2 Morph Methods: Difference between revisions
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m added How to save orientation of multiple models in PyMol |
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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 (symmetry operations until the SYMOP functions within Jmol work within Proteopedia when newer version added) 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). | 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 - 'set all_states,0' turns it back to one frame only shown). | ||
From http://www.mail-archive.com/pymol-users@lists.sourceforge.net/msg02004.html | 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> | found this series of commands (ENTERED ONE LINE AT A TIME) helped make a file with all models from PyMOL:<br> | ||
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cmd.extend('save_transformed',save_transformed) | cmd.extend('save_transformed',save_transformed) | ||
</pre> | </pre> | ||
And so I again loaded the 3kg2 a to b morph (assigned secondary structure so cartoon look matched what I was used to looking at) and oriented like I wanted, then split them all and deleted original using commands above up until 'rewind' command, then ran the script I had saved on my drive, and then typed 'save_transformed all, test.pdb' | |||
