Re: [PyMOL] help with PyMOL rename command

[Norbert S. <st...@bb...>]

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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