Re: [PyMOL] Changing of atom order after superimposition

[James S. <jms...@gm...>]

hmm using TMalign method of superimposition I've solved that problem (
the atom order  of ligand have been unchanged).


James

2013/2/7 James Starlight <jms...@gm...>:
> Dear PyMol users!
>
> I've forced with the problem during superimposition of two identical
> proteins. First of all I've defined in pymol
>
> set retain_order,1
> set pdb_retain_ids,1
>
> to prevent changing of atom order after editing.
>
> than I do super system1, system2
>
> and obtain changed atom order in system1 which have been moved ( in
> particular in ligand's coordinates which are present in that system
> but absent in the reference system2).
>
>
> How I could fix it ?
>
>
> James