Re: [PyMOL] Distances and Python scripts

[Andreas H. <ah...@bi...>]

Hi Xavier,

here is a naive approach to solve problem 2), which should include your 
first problem.
#########################################################################
from pymol import cmd, stored

## setup
myProt = "2gsm"
mySegm = ""
myChain = "B"
cmd.fetch(myProt)
outfile = open("/tmp/n_n_distances.txt", "w")

selection = "/%s/%s/%s/*/N" % (myProt, mySegm, myChain)

## getting the atoms of a selection
stored.list = []
cmd.iterate(selection, "stored.list.append((resi, name))")
print len(stored.list)

for atom1 in stored.list:
for atom2 in stored.list:
selection1 = "/%s/%s/%s/%s/%s" % (myProt, mySegm, myChain, atom1[0], 
atom1[1])
selection2 = "/%s/%s/%s/%s/%s" % (myProt, mySegm, myChain, atom2[0], 
atom2[1])
distance = cmd.distance("d", selection1, selection2, cutoff = 6.0)
if distance > 0.0: ## distance can be 0, if atom1==atom2 or if atom1 and 
atom2 are more than 6A apart
print >> outfile, selection1, selection2, distance
outfile.close()
########################################################################
produces a file like this:

## /2gsm//B/31/N /2gsm//B/30/N 3.59292006493
## /2gsm//B/31/N /2gsm//B/32/N 3.55046916008
## /2gsm//B/31/N /2gsm//B/246/N 5.16704130173

I hope perfomance doesnt matter, since this is quite slow.
Otherwise I suggest to use get_model to get a list of coordinates and 
put them into a distance matrix, eg. using scipy:
http://aspn.activestate.com/ASPN/Cookbook/Python/Recipe/498246
let me know if this is what you want.

I hope that helps!

Best regards,
Andreas

Xavier HANOULLE wrote:
> Hi all,
>
> I have 2 problems regarding the distance command and python scripting:
>
> *1/* I would like to use a script in order to print in a file the 
> results of this following command:
> distance dist6, (/MyProt/MyProt/A/181/N), (/MyProt/MyProt/A/*/N), 6.0
> This command displays distances and dash lines between the N atom of 
> residue 181 and all the N atoms of MyProt which are at <6Ang. How do I 
> have to write a Python script to get the results in a text file that 
> will look like:
> /MyProt/MyProt/A/181/N /MyProt/MyProt/A/180/ 4.856
> /MyProt/MyProt/A/181/N /MyProt/MyProt/A/182/ 3.956
> /MyProt/MyProt/A/181/N /MyProt/MyProt/A/78/ 5.562
> /MyProt/MyProt/A/181/N /MyProt/MyProt/A/105/ 2.863
> ... ?
>
>
> *2/ *How do I have to write a python script to measure all the N-N 
> distances in my protein and to print the results in a text file that 
> will look like:
> /MyProt/MyProt/A/1/N /MyProt/MyProt/A/2/ 4.856
> /MyProt/MyProt/A/1/N /MyProt/MyProt/A/3/ 3.956
> /MyProt/MyProt/A/1/N /MyProt/MyProt/A/4/ 5.562
> ...
> /MyProt/MyProt/A/2/N /MyProt/MyProt/A/1/ 3.857
> /MyProt/MyProt/A/2/N /MyProt/MyProt/A/3/ 7.249
> /MyProt/MyProt/A/2/N /MyProt/MyProt/A/4/ 8.762
> ... ?
> Furthermore, would it be possible to add a limit for these distances ? 
> For exemple, only get the N-N distances in MyProt which are <7Ang. ?
>
> Thanks for your help.
> Sincerely,
>
> Xavier.
>
> *
> ------------------------------------------------------------------------
> *
>
> *Xavier HANOULLE, Ph.D.*
>
> UMR 8576 CNRS–USTL
> Structural and Functional Glycobiology Unit
> NMR Laboratory
> 59655 Villeneuve d’Ascq Cedex - France
>
> Phone: +33 (0)3.20.33.72.41
> E-mail : xav...@un... 
> <mailto:xav...@un...>
> www: http://groupe-rmn-modelisation.univ-lille1.fr 
> <http://groupe-rmn-modelisation.univ-lille1.fr/>
>
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-- 
Andreas Henschel
Bioinformatics Group
TU Dresden
Tatzberg 47-51
01307 Dresden, Germany

Phone: +49 351 463 40063
EMail: ah...@bi...