User:Wayne Decatur/3kg2 Morph Methods: Difference between revisions
From Proteopedia
Jump to navigationJump to search
mNo edit summary |
mNo edit summary |
||
| Line 2: | Line 2: | ||
<br> | <br> | ||
for example:<br> | for example:<br> | ||
< | <pre> | ||
alter (chain B),chain='A' | alter (chain B),chain='A' | ||
sort | sort | ||
</ | </pre> | ||
| Line 15: | Line 15: | ||
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> | ||
< | <pre> | ||
split_states 3kg2atob | split_states 3kg2atob | ||
delete 3kg2atob | delete 3kg2atob | ||
| Line 21: | Line 21: | ||
rewind | rewind | ||
save test.pdb, all | save test.pdb, all | ||
</ | </pre> | ||
'''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> | '''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> | ||
< | <pre> | ||
# Adds the command save_transformed | # Adds the command save_transformed | ||
# Usage: save_transformed object, file | # Usage: save_transformed object, file | ||
| Line 37: | Line 37: | ||
cmd.extend('save_transformed',save_transformed) | cmd.extend('save_transformed',save_transformed) | ||
</ | </pre> | ||
