In addition I'd like to know more about possible flexibility in the representation of the protein-ligand contacts by means of the present-> ligand site option.

For instance sometimes I have ligand group situated in the some distance from the interiour group. So this space forms empty cavity around ligand. So if I use present- ligand sites by default pymol didnt see the interiour residues due to its remoteness from ligand. But could I vary some cutoff distance to represent POSSIBLE polar and packing contacts like as this interiour would be in the contact with the ligand? I'd like to use this for better prediction of the mutations wich will change the shape and geometry of the ligand binding pockets in the above cases. \

Thanks again,


2012/1/23 James Starlight <>
Thanks Thomas

The reversible convertion indeed solved problem.


2012/1/23 Thomas Holder <>
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"
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


Thomas Holder
MPI for Developmental Biology
Spemannstr. 35
D-72076 Tübingen