User:Wayne Decatur/3kg2 Morph Methods
From Proteopedia
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<br> | <br> | ||
for example:<br> | for example:<br> | ||
| - | alter (chain B),chain='A' | + | <source lang="python"> |
| - | sort< | + | alter (chain B),chain='A' |
| + | sort | ||
| + | </source> | ||
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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> | found this series of commands (ENTERED ONE LINE AT A TIME) helped make a file with all models from PyMOL:<br> | ||
<br> | <br> | ||
| - | + | <source lang="python"> | |
| - | delete 3kg2atob | + | split_states 3kg2atob |
| - | alter all, segi = model[-4:] | + | delete 3kg2atob |
| - | rewind | + | alter all, segi = model[-4:] |
| - | save test.pdb, all< | + | rewind |
| + | save test.pdb, all | ||
| + | </source> | ||
| - | '''However, this didn't save the orientation I had moved it to at the start.''' | + | '''However, this didn't save the orientation I had moved it to at the start.''' Seems I could use [http://pymolwiki.org/index.php/Get_View get_view] and [http://pymolwiki.org/index.php/Set_View set_view] commands to get back to what I wanted after reload but I need it to open in Jmol the way I wanted so that doesn't help. A little more searching turned up on the [http://pymolwiki.org/index.php/Modeling_and_Editing_Structures Modeling and Editing Structures page of the PyMol Wiki] that I could save with transformed coordinates using a simple Python script:<br> |
| + | <source lang="python"> | ||
| + | # Adds the command save_transformed | ||
| + | # Usage: save_transformed object, file | ||
| + | def save_transformed(object,file): | ||
| + | m = cmd.get_view(0) | ||
| + | ttt = [m[0], m[1], m[2], 0.0, | ||
| + | m[3], m[4], m[5], 0.0, | ||
| + | m[6], m[7], m[8], 0.0, | ||
| + | 0.0, 0.0, 0.0, 1.0] | ||
| + | cmd.transform_object(object,ttt) | ||
| + | cmd.save(file,object) | ||
| + | |||
| + | cmd.extend('save_transformed',save_transformed) | ||
| + | </source> | ||
Revision as of 16:52, 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:
<source lang="python">
alter (chain B),chain='A'
sort
</source>
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:
<source lang="python">
split_states 3kg2atob
delete 3kg2atob
alter all, segi = model[-4:]
rewind
save test.pdb, all
</source>
However, this didn't save the orientation I had moved it to at the start. Seems I could use get_view and set_view commands to get back to what I wanted after reload but I need it to open in Jmol the way I wanted so that doesn't help. A little more searching turned up on the Modeling and Editing Structures page of the PyMol Wiki that I could save with transformed coordinates using a simple Python script:
<source lang="python">
- Adds the command save_transformed
- Usage: save_transformed object, file
def save_transformed(object,file):
m = cmd.get_view(0)
ttt = [m[0], m[1], m[2], 0.0,
m[3], m[4], m[5], 0.0,
m[6], m[7], m[8], 0.0,
0.0, 0.0, 0.0, 1.0]
cmd.transform_object(object,ttt)
cmd.save(file,object)
cmd.extend('save_transformed',save_transformed) </source>
