Hi Katherine,
PyMOL can do what you want. I've done this exact task before.
Here's the idea. If you have a PDB with multiple ligands and you use,
select allLigands, organic and myProtein
you create the selection allLigands which contains all the ligand
atoms in myProtein. What you need to do is extract each ligand,
molecule by molecule, from the allLigands selection using selection
algebra until myLigands is empty. It's done like this:
# create a selection containing the atoms of all ligands
select allLigands, organic and myProtein
# create a selection to use later as we iterate across
# all ligands, this will hold individual ligands we extract
# from allLigands
select current_ligand, none
# enter a Python block so we can use Python while-loop
# and other Python syntax
python
# loop until allLigands is not empty
while cmd.count_atoms("myLigands") > 0:
# copy the first ligand selection, by molecule, into
# the, "current_ligand"
cmd.select("current_ligand", "bm. first allLigands")
# do something with "current_ligand", like finding all ligands
# without waters nearby
if cmd.count_atoms("solvent within 5 of current_ligand") == 0:
print "This is an interesting ligand."
# now remove current_ligand from allLigands
# and loop again
cmd.select("allLigands", "allLigands and not current_ligand")
python end
Good luck!
Cheers,
-- Jason
On Fri, Dec 13, 2013 at 4:58 PM, Katherine Sippel
<katherine.sip...@gmail.com> wrote:
> Hi Carsten,
>
> Thanks for the help. I've tried variants of that selection and it works
> great if there is only one ligand. Unfortunately it breaks down when there
> are multiple ligands and they don't all fit the criteria. I'm surveying
> almost half the PDB so these are all different proteins with different
> binding sites and ligands. I was hoping for a way to get pymol to recognize
> each individual ligand automatically by grouping common resids within the
> non-solvent hetatm selection. Using the %s %(resi) seems to require an
> explicit input.
>
> I might be able to extract an explicit chain/resi designation for each file
> from the het portion of the pdb header, though I'm not sure how to automate
> this. I suppose it's back to the script repository for me.
>
> Cheers,
> Katherine
>
>
> On Fri, Dec 13, 2013 at 2:50 PM, Schubert, Carsten [JRDUS]
> <cschu...@its.jnj.com> wrote:
>>
>> Katherine,
>>
>>
>>
>> not sure if that is what you are looking for but you can select for
>> non-polymer residues with:
>>
>>
>>
>> select lig, prot and organic
>>
>>
>>
>> That will select any non polymer (protein and R(D)NA) residues present in
>> the pdb. You then would need to break the selection further into the
>> individual constituents, by either chain Id and resid.
>>
>>
>>
>> Hope this helps a bit.
>>
>>
>>
>> Carsten
>>
>>
>>
>> From: Katherine Sippel [mailto:katherine.sip...@gmail.com]
>> Sent: Friday, December 13, 2013 10:28 AM
>> To: pymol-users@lists.sourceforge.net
>> Subject: [PyMOL] Selection algebra issue
>>
>>
>>
>> Hi all,
>>
>> I'm trying to write a script to data mine the pdb. I'm want to look at the
>> ligands in a pdb file and fish out those that meet a certain criteria. I've
>> got a script that can look at the ligands all at once but I need to assess
>> each ligand individually. Since I'm looking at 40,000+ pdbs I need a way to
>> define them individually. I've tried variations on "%s' % (resi)" and
>> "bymolec" but I can't seem to figure out how to get them parsed separately
>> without specifying a number. I've also tried using index to create a tuples
>> list and iterating from that but I keep hitting the same issue. I've
>> attached a couple of the attempted scripts so you can laugh at my google
>> derived python skills.
>>
>> I've been trying to figure this out for a week now and I'm completely
>> stumped. If anyone could nudge me in the right direction, even if it's some
>> Pymolwiki article I missed, I would appreciate it immensely.
>>
>> Thanks for your time,
>> Katherine
>>
>>
>> --
>>
>> "Nil illegitimo carborundum" - Didactylos
>
>
>
>
> --
> "Nil illegitimo carborundum" - Didactylos
>
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(e) jason.vertr...@schrodinger.com
(o) +1 (603) 374-7120
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