ToGroup
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Overview
toGroup will convert a multistate object into a group of single-state objects. Be warned, by default it deletes your original object (since it's extracting a copy).
PyMOL does a great job at handling multistate objects and grouping them together. One thing that I found myself doing over and over again was
- loading a multistate object (say a PDBQT file with 100 ligand poses)
- splitting that object into all 100 states, with some given prefix
- then grouping them into their own group
- and then finally removing the original.
This became tedious, so I automated that with this script.
Examples
# A multistate object (20 NMR states) fetch 1nmr # Create the group called, "nmrEnsemble" # from '1nmr' and name all the new states state1, # state2, state3, etc. toGroup nmrEnsemble, 1nmr, prefix=state
The Code
import pymol from pymol import cmd def toGroup(groupName,sel,prefix="",delOrig=True): """ DESCRIPTION toGroup will take a multistate object and extract it to a group with N objects all in state #1. It essentially performs the following: split_states myObj, prefix=somePrefix group newGroup, somePrefix* delete myObj PARAMETERS: groupName (string) The name of the group to create sel (string) The name of the selection/object from which to make the group prefix (string) The prefix of the names of each of split states. For example, if your prefix is ''obj'' and is in states 1 through 100 then the states will be labeled obj1, obj2, obj3, ..., obj100. delOrig (string/boolean) If true then delete the original selection, otherwise not. RETURN Nothing, it makes a new group. """ if prefix=="": prefix="grouped" cmd.split_states(sel, prefix=prefix) cmd.group(groupName,prefix+"*") if delOrig: cmd.delete(sel) cmd.extend("toGroup", toGroup)
See Also
group, select,, split_states, delete, extend.
