Hi Elsa,
Good first attempt. "cmd.distance" will return the distance between
two atoms or the average distance if you give it more than two. Most
surely your "chain A" and "chain C" each have more than one atom each.
So, you just get the average distance.
I'm not sure what exact distances you want to measure: all atoms;
alpha carbons; average chain? If you want to measure the distances
between all M atoms in chain A and all N atoms in chain B, you get an
MxN matrix of distances by the following code:
python
from pymol import stored
stored.a, stored.b = [], []
cmd.iterate_state(1, "chain A", "stored.a.append(ID)")
cmd.iterate_state(1, "chain B", "stored.b.append(ID)")
outFile = open("/tmp/distances", 'w')
for a in stored.a:
for b in stored.b:
outFile.write( "distance from %s to %s is %s\n" % (a, b,
cmd.distance( "id %s" % a, "id %s" % b)))
outFile.close()
python end
Now read your file, "/tmp/distances".
If you want average positions between chain A and B, then you need to
compute the center of mass
(http://pymolwiki.org/index.php/Center_Of_Mass), create two
pseudoatoms (http://pymolwiki.org/index.php/Pseudoatom) at the centers
of mass, and calculate that distance.
Cheers,
-- Jason
On Wed, Jul 14, 2010 at 8:26 AM, <elsa.liv...@irb.unisi.ch> wrote:
> Hello,
> I used a simple script to calculate the distance between
> two objects called chain_a and chain_c in the range of 1
> A,
> graphically the script works and in the monitor is
> possible observe the distance and the residues involved,
> I have some problems to print out the distance values and
> the residues involved in a .txt file.
> The script that I used
> is very simple, the txt file is created but inside there
> is just one distance and I don't know how insert also
> the residues involved,
> do you have some idea or suggestion
> the script is:
>
> # import PyMOL's command namespace
> from pymol import cmd
>
> # open dist.txt for writing
> f=open('dist.txt','w')
>
> # calculate the distance and store it in dst
> dst=cmd.distance('tmp','chain_a','chain_c',1)
>
> # write the formatted value of the distance (dst)
> # to the output file
> f.write("%8.3f\n"%dst)
>
> # close the output file.
> f.close()
>
> Thanks a lot
> Elsa
>
> ------------------------------------------------------------------------------
> This SF.net email is sponsored by Sprint
> What will you do first with EVO, the first 4G phone?
> Visit sprint.com/first -- http://p.sf.net/sfu/sprint-com-first
> _______________________________________________
> PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net)
> Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users
> Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
>
--
Jason Vertrees, PhD
PyMOL Product Manager
Schrodinger, LLC
(e) jason.vertr...@schrodinger.com
(o) +1 (603) 374-7120
------------------------------------------------------------------------------
This SF.net email is sponsored by Sprint
What will you do first with EVO, the first 4G phone?
Visit sprint.com/first -- http://p.sf.net/sfu/sprint-com-first
_______________________________________________
PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net)
Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users
Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
