pymol-users

[PyMOL] script to write down distances ligand-protein: need feedback

[Andrea S. <and...@gm...>]

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 =3D {}
    FileToOpen =3D 'Dist' + number=20
    DistOutput =3D open(FileToOpen,'w')
    DistOutput.write("ATOM_PROTEIN ATOM_LIGAND DISTANCE\n")
    out =3D open('cluster.out','r')
    pro_atoms =3D cmd.get_model("ref")
# read cluster file
    for i in out.readlines():
        i=3Dstring.strip(i)      =20
        tmp =3D string.split(i," ")
        index, elems =3D tmp[1], tmp[3:len(tmp)] =20
        HoL[index] =3D elems
# visualize the structures of cluster number
    for eachElem in HoL[number]:
        newElem =3D 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 =3D cmd.select('don','(elem n,o and (neighbor hydro))')
        Acc =3D cmd.select('acc','(elem o or (elem n and not (neighbor hydr=
o)))')
#     atoms_Don =3D cmd.index('don')
#     atoms_Acc =3D cmd.index('acc')
        HBA =3D cmd.distance('(lig and acc)','(active and don)',3.2)
        HBD =3D cmd.distance('(lig and don)','(active and acc)',3.2)
        cmd.align('ref',eachElem)
        DistOutput.write(" %14s  %14s %8.3f\n"%(Don,Acc,HBA))
    =20
    DistOutput.close()
=20
cmd.extend('read_cluster',read_cluster)
########## CUT HERE ################

Re: [PyMOL] script to write down distances ligand-protein: need feedback

[Gilleain T. <gil...@ho...>]

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" <and...@gm...> 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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Re: [PyMOL] script to write down distances ligand-protein: need feedback

[Andrea S. <and...@gm...>]

>   HBA =3D cmd.distance('HBA', '(lig and acc)','(active and don)', 3.2)
yes thanks for the trick. However, I edited my script to:
DistOutput.write(" %14s  %14s %8s %8s\n"%("donor","acceptor","hba","hbd"))
DistOutput.write(" %14s  %14s %8.3f %8.3f\n"%(Don,Acc,HBA,HBD))
but I cannot figure out the meaning of the output:
complex_1
          donor        acceptor      hba      hbd
            260             271    2.536   -1.000
complex_2
          donor        acceptor      hba      hbd
            391             409    2.489   -1.000
complex_3
          donor        acceptor      hba      hbd
            522             547    2.512   -1.000
complex_4
          donor        acceptor      hba      hbd
            653             685    2.456   -1.000
what the numbers under donor and acceptor are?

>=20
>   atoms_Don =3D cmd.index('don')
>=20

I tried also this option and it works fine (more or less) excet that
it takes a lot time to calculate all the distance (quite weird on my
dual-cpu 3Gz intel)
this is the loop used:
   for donor in atoms_Don:
            for acceptor in atoms_Acc:
                di =3D cmd.get_distance("%s`%d"%donor,"%s`%d"%acceptor)
                DistOutput.write("%8s %8s %8.3f\n"%(donor,acceptor,di))

thanks

Regards

andrea

Re: [PyMOL] script to write down distances ligand-protein: need feedback

[Gilleain T. <gil...@ho...>]

Hi,

I suppose that these numbers are the atom_ids. It's probably the same
numbers returned by the cmd.index function.

I guess you could test this by typing "select atom260, id 260" and see if
that makes a selection with atom260...

As for the speed question, I have no idea. More of a question for Mr DeLano
:) Calculating pairwise like this is always going to be computationally
expensive, but I don't know ways to speed this up.

gilleain torrance


On 5/7/05 15:17, "Andrea Spitaleri" <and...@gm...> wrote:

>>   HBA = cmd.distance('HBA', '(lig and acc)','(active and don)', 3.2)
> yes thanks for the trick. However, I edited my script to:
> DistOutput.write(" %14s  %14s %8s %8s\n"%("donor","acceptor","hba","hbd"))
> DistOutput.write(" %14s  %14s %8.3f %8.3f\n"%(Don,Acc,HBA,HBD))
> but I cannot figure out the meaning of the output:
> complex_1
>           donor        acceptor      hba      hbd
>             260             271    2.536   -1.000
> complex_2
>           donor        acceptor      hba      hbd
>             391             409    2.489   -1.000
> complex_3
>           donor        acceptor      hba      hbd
>             522             547    2.512   -1.000
> complex_4
>           donor        acceptor      hba      hbd
>             653             685    2.456   -1.000
> what the numbers under donor and acceptor are?
> 
>> 
>>   atoms_Don = cmd.index('don')
>> 
> 
> I tried also this option and it works fine (more or less) excet that
> it takes a lot time to calculate all the distance (quite weird on my
> dual-cpu 3Gz intel)
> this is the loop used:
>    for donor in atoms_Don:
>             for acceptor in atoms_Acc:
>                 di = cmd.get_distance("%s`%d"%donor,"%s`%d"%acceptor)
>                 DistOutput.write("%8s %8s %8.3f\n"%(donor,acceptor,di))
> 
> thanks
> 
> Regards
> 
> andrea
> 
> 
> -------------------------------------------------------
> SF.Net email is sponsored by: Discover Easy Linux Migration Strategies
> from IBM. Find simple to follow Roadmaps, straightforward articles,
> informative Webcasts and more! Get everything you need to get up to
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> 

Re: [PyMOL] script to write down distances ligand-protein: need feedback

[Andrea S. <and...@gm...>]

Hi
thanks for your reply. Yes it is the id.
I found out also that it takes a lot time because is looping in all
atoms and in the "active" site. So I fixed that.
Anyway more in general, I saw that the manual is lacking of some
information useful for who wants to program. I mean, sometimes it
doesn't say if a command returns a tuple or a list or a dictionary.
Ex:
cmd.index("selection") is a list?

thanks

Regards,

andrea

2005/7/6, Gilleain Torrance <gil...@ho...>:
> Hi,
>=20
> I suppose that these numbers are the atom_ids. It's probably the same
> numbers returned by the cmd.index function.
>=20
> I guess you could test this by typing "select atom260, id 260" and see if
> that makes a selection with atom260...
>=20
> As for the speed question, I have no idea. More of a question for Mr DeLa=
no
> :) Calculating pairwise like this is always going to be computationally
> expensive, but I don't know ways to speed this up.
>=20
> gilleain torrance
>=20
>=20
> On 5/7/05 15:17, "Andrea Spitaleri" <and...@gm...> wrote:
>=20
> >>   HBA =3D cmd.distance('HBA', '(lig and acc)','(active and don)', 3.2)
> > yes thanks for the trick. However, I edited my script to:
> > DistOutput.write(" %14s  %14s %8s %8s\n"%("donor","acceptor","hba","hbd=
"))
> > DistOutput.write(" %14s  %14s %8.3f %8.3f\n"%(Don,Acc,HBA,HBD))
> > but I cannot figure out the meaning of the output:
> > complex_1
> >           donor        acceptor      hba      hbd
> >             260             271    2.536   -1.000
> > complex_2
> >           donor        acceptor      hba      hbd
> >             391             409    2.489   -1.000
> > complex_3
> >           donor        acceptor      hba      hbd
> >             522             547    2.512   -1.000
> > complex_4
> >           donor        acceptor      hba      hbd
> >             653             685    2.456   -1.000
> > what the numbers under donor and acceptor are?
> >
> >>
> >>   atoms_Don =3D cmd.index('don')
> >>
> >
> > I tried also this option and it works fine (more or less) excet that
> > it takes a lot time to calculate all the distance (quite weird on my
> > dual-cpu 3Gz intel)
> > this is the loop used:
> >    for donor in atoms_Don:
> >             for acceptor in atoms_Acc:
> >                 di =3D cmd.get_distance("%s`%d"%donor,"%s`%d"%acceptor)
> >                 DistOutput.write("%8s %8s %8.3f\n"%(donor,acceptor,di))
> >
> > thanks
> >
> > Regards
> >
> > andrea
> >
> >
> > -------------------------------------------------------
> > SF.Net email is sponsored by: Discover Easy Linux Migration Strategies
> > from IBM. Find simple to follow Roadmaps, straightforward articles,
> > informative Webcasts and more! Get everything you need to get up to
> > speed, fast. http://ads.osdn.com/?ad_idt77&alloc_id=16492&op=3Dclick
> > _______________________________________________
> > PyMOL-users mailing list
> > PyM...@li...
> > https://lists.sourceforge.net/lists/listinfo/pymol-users
> >
>=20
> -------------------------------------------------------
> SF.Net email is sponsored by: Discover Easy Linux Migration Strategies
> from IBM. Find simple to follow Roadmaps, straightforward articles,
> informative Webcasts and more! Get everything you need to get up to
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k
> _______________________________________________
> PyMOL-users mailing list
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> https://lists.sourceforge.net/lists/listinfo/pymol-users
>