User:Wayne Decatur/3kg2 Morph Methods
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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 | + | 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 | 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> | ||
<br> | <br> | ||
| - | split_states 3kg2atob | + | split_states 3kg2atob<br> |
| - | delete 3kg2atob | + | delete 3kg2atob<br> |
| - | alter all, segi = model[-4:] | + | alter all, segi = model[-4:]<br> |
| - | rewind | + | rewind<br> |
| - | save test.pdb, all | + | save test.pdb, all<br> |
| + | |||
| + | '''However, this didn't save the orientation I had moved it to at the start.''' | ||
Revision as of 16:43, 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 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.
