[Kaushik Raha]
> If you have a PDB file of the ligands and know the number of atoms in
> each ligand, then you could introduce a TER card after the each ligand.
> That way PyMOL will not draw bonds between the ligands.
That's not quite enough; PyMOL still draws bonds for me. I seem to recall
something about PyMOL wanting non-consecutive residue IDs to ensure that
things don't get bonded together, but that's still not enough:
select nonprot, resi 160-660
alter (nonprot),resi=str(int(resi*2))
save thing.pdb
delete all
load thing.pdb
still produced the unwanted bonds (and I made sure that there were still
TER cards)
[Kristian Rother]
> Did you try to split up the file into smaller ones? This should do it.
I wrote a cool script that split a file up into chunks on the fly and used
read_pdbstr to load the chunks separately. Unfortunately, PyMOL was
really slow when dealing with so many objects (it was faster to do the
cmd.do('unbond...')).
any other ideas?
thanks,
-michael
> On Tuesday 17 August 2004 17:02, Michael George Lerner wrote:
> > to the protein, but not to eachother. So, lots of the ligands overlap.
> > When PyMOL sees this, it draws bonds between the ligands. Every time I
> > load up one of these structures, I have to unbond things
