Hi James,
> I have no problems with the representation of the assigned ligand with
> its environment but when I save this as new pdb via
>
> save test.pdb, visible
>
> my output pdb contains some errors like missing bonds between HETATM
> residues ( ligand ) etc.
maybe this trick was too dirty... change the type back to ATOM before
saving:
select motif, (pepseq TYG) and not (name C+N+O)
alter motif, type="HETATM"
preset.ligand_cartoon("all")
alter motif, type="ATOM"
> Also I've checked this new pdb and find alot of
> TER strings between each of residues.
This is because you only selected the local environment which has only
short pieces of the polymer. PyMOL sees chain breaks there. You can
suppress TER records by:
unset pdb_use_ter_records
Cheers,
Thomas
--
Thomas Holder
MPI for Developmental Biology
Spemannstr. 35
D-72076 Tübingen
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