Hi,
Well, the cmd.distance method seems to take minimum 4 parameters, not three:
cmd.distance( string name, string selection1, string selection2, string
cutoff, string mode )
where 'mode' is not important.
So, in the script you give, the line:
HBA = cmd.distance('(lig and acc)','(active and don)',3.2)
could become
HBA = cmd.distance('HBA', '(lig and acc)','(active and don)', 3.2)
or, if you use the atom ids that you get from the (commented out) lines:
atoms_Don = cmd.index('don')
you could use cmd.get_distance in a loop:
for donor in atoms_Don:
for acceptor in atoms_Acc:
DistOut.write("%s" % cmd.get_distance(donor, acceptor))
or something.
gilleain torrance
On 5/7/05 11:50, "Andrea Spitaleri" <[email protected]> wrote:
> Hi guys,
> I am trying to make a script to automatize a procedure. I have got a
> file where I can pick up the structure of protein-ligand complexes
> cluster
> The script below read the number of the cluster and then visualize
> them align with a protein reference. Everything is fine except I'd
> like write on a file the distances between some residues of each
> structure with the ligand but I cannot figure out how do it. I read
> different post but it seems that I missing something.
>
> thanks a lot
>
> Regards,
>
> andrea
>
> ##### CUT HERE #####
> from pymol import cmd
> import string, sys, os
>
> def read_cluster(number):
> cmd.reinitialize()
> cmd.load('/home/pippo/ref.pdb','ref')
> cmd.select('Refactive','resi 17+20+23+25+26+43+44 in ref')
> HoL = {}
> FileToOpen = 'Dist' + number
> DistOutput = open(FileToOpen,'w')
> DistOutput.write("ATOM_PROTEIN ATOM_LIGAND DISTANCE\n")
> out = open('cluster.out','r')
> pro_atoms = cmd.get_model("ref")
> # read cluster file
> for i in out.readlines():
> i=string.strip(i)
> tmp = string.split(i," ")
> index, elems = tmp[1], tmp[3:len(tmp)]
> HoL[index] = elems
> # visualize the structures of cluster number
> for eachElem in HoL[number]:
> newElem = eachElem + '.pdb'
> cmd.load(newElem.strip(),eachElem)
> cmd.select('active','resi 17+20+23+25+26+43+44')
> cmd.select('lig','resn CBO')
> cmd.select('ligDon','(elem n,o and (neighbor hydro) in lig)')
> cmd.select('ligAcc','(elem o or (elem n and not (neighbor
> hydro)) in lig)')
> Don = cmd.select('don','(elem n,o and (neighbor hydro))')
> Acc = cmd.select('acc','(elem o or (elem n and not (neighbor
> hydro)))')
> # atoms_Don = cmd.index('don')
> # atoms_Acc = cmd.index('acc')
> HBA = cmd.distance('(lig and acc)','(active and don)',3.2)
> HBD = cmd.distance('(lig and don)','(active and acc)',3.2)
> cmd.align('ref',eachElem)
> DistOutput.write(" %14s %14s %8.3f\n"%(Don,Acc,HBA))
>
> DistOutput.close()
>
> cmd.extend('read_cluster',read_cluster)
> ########## CUT HERE ################
>
>
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