Dear wdela,
usually each atom in a residue has a different atom name. If this is not
the case, the rename command will rename the atoms, that do not have
unique names within a residue. It appears as if you cannot specify which
atom names the renamed atoms will get. If you want to change to specific
atom names, use a text editor.
Say ligand.pdb contains a molecule with some identically named atoms.
load ligand.pdb, ligand
rename ligand
This will automatically rename atoms to ensure unique atom names.
select mysel, ligand and name CA
rename mysel
Will only rename atoms CA to ensure unique atoms names.
You can apply the command to objects or selections.
Best wishes,
Norbert
Am 01.10.2023 um 17:28 schrieb wdela--- via PyMOL-users:
Hi need help with PyMOL rename command:
from https://pymolwiki.org/index.php/Rename :
Rename
*rename* creates new atom names which are unique within residues.
USAGE
CURRENT
rename object-name [ ,force ]
force = 0 or 1 (default: 0)
PROPOSED
rename object-or-selection,force
NOTES
To regerate only some atom names in a molecule, first clear them with
an "alter (sele),name=/“ commmand, then use "rename”/
...........................................................................................
Does 'rename test' create 'test' atom name ?? If so how do I apply it
to a selection ? I know how to use set_name to change an
object/selection name : https://pymolwiki.org/index.php/Set_name or
alter to change a property over a selection :
https://pymolwiki.org/index.php?title=Alter&redirect=no Cannot figure
out how rename works
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