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User:Wayne Decatur/3kg2 Morph Methods

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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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&nbsp:<br>
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&nbsp;<br>
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.
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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).
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From http://www.mail-archive.com/pymol-users@lists.sourceforge.net/msg02004.html
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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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&nbsp;<br>
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split_states 3kg2atob
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delete 3kg2atob
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alter all, segi = model[-4:]
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rewind
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save test.pdb, all

Revision as of 16:40, 10 July 2010

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 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:
 
split_states 3kg2atob delete 3kg2atob alter all, segi = model[-4:] rewind save test.pdb, all

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Wayne Decatur

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