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. \
The reversible convertion indeed solved problem.
James2012/1/23 Thomas Holder <firstname.lastname@example.org>
Hi James,maybe this trick was too dirty... change the type back to ATOM before saving:
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.
select motif, (pepseq TYG) and not (name C+N+O)
alter motif, type="HETATM"
alter motif, type="ATOM"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:
Also I've checked this new pdb and find alot of
TER strings between each of residues.
MPI for Developmental Biology