Hej Suzanne, 

you will need to append the other two distances to the script to get them printed.
Following your example that would be something like:

# calculate the distance and store it in dst
dst2=cmd.distance('tmp','B///297/cb','A///17-19/cb') # change the selections in this line!
dst3=cmd.distance('tmp','B///297/cb','A///17-19/cb') # change the selections in this line!

# and then for writing the output file

inserting these blocks in your script hopefully will do the trick.



On Tue, Jun 17, 2014 at 8:21 PM, Lapolla, Suzanne M (HSC) <suzanne-lapolla@ouhsc.edu> wrote:
Another follow up question to this. I decided to use the measure distance python script on the pymol wiki to do this, and I was able to do it successfully with a range of residues, but my question is about the output txt file.  When I run the script I get the correct distances (all 3 of them) to show on the GUI but the text file that is generated (distnew.txt) only lists one distance--so perhaps the script needs to be modified for this as well for the residues measured?

The original script is at the link http://www.pymolwiki.org/index.php/Measure_Distance
and my modified version is below. Suggestions appreciated! Thank you.

# This script writes the distance from
# atom mol1///25/ha to atom mol1///26/ha
# out to the file "dist.txt"
# Simply change your selections to see different distances.

# import PyMOL's command namespace
from pymol import cmd

# open dist.txt for writing

# calculate the distance and store it in dst

# write the formatted value of the distance (dst)
# to the output file

# close the output file.
From: Robert Campbell [robert.campbell@queensu.ca]
Sent: Monday, June 09, 2014 10:04 AM
To: pymol-users@lists.sourceforge.net
Subject: Re: [PyMOL] command question RE printing out distances to text file

Hi Suzanne,

You can also get the distance printed in the external GUI or terminal window
by using the "cmd.distance" version of the command.  So either you can
assign the distance to a variable and print it or you can print the result

Assuming you have two selections, sele1 and sele2 specifying the atoms of
interest you can do:

  d = cmd.distance(sele1,sele2)
  print sele1,sele2,d


On Mon, 2014-06-09
13:13 EDT, Thomas Holder <thomas.holder@schrodinger.com> wrote:

> Hi Suzanne,
> you can use the get_distance command. It doesn't generate a distance
> object but prints the distance to the external window.
> https://urldefense.proofpoint.com/v1/url?u=http://pymolwiki.org/index.php/Get_Distance&k=7DHVT22D9IhC0F3WohFMBA%3D%3D%0A&r=1ciN0EuZ9XNq3lPnYtgkI5sKPXgKVaywidBN0C981SQ%3D%0A&m=fr2bAoLQoVgp9h2t2fgBvfGVVX7oQ1g14g1AODFz%2FRg%3D%0A&s=921f4dfed39cd38f4ae7a70dfb937844d4e3faf1bc967c2f4d1f2944fa2ea31b
> Cheers,
>   Thomas
> On 06 Jun 2014, at 23:03, Lapolla, Suzanne M (HSC)
> <suzanne-lapolla@ouhsc.edu> wrote:
> > Fellow Pymol Users:
> > I may have asked this question before...but if so have forgotten. I am
> > measuring distances between 2 atoms in 2 different objects using the
> > distance command, and it is working perfectly, but I wonder if there is
> > a command I can use/add so that those distances can be printed in the
> > external gui as well as being shown in the viewer. I will be doing lots
> > of these at the same time and the screen will get crowded. Thank you in
> > advance.

Robert L. Campbell, Ph.D.
Senior Research Associate/Adjunct Assistant Professor
Dept. of Biomedical & Molecular Sciences
Botterell Hall Rm 644
Queen's University,
Kingston, ON K7L 3N6  Canada
Tel: 613-533-6821
<robert.campbell@queensu.ca>    https://urldefense.proofpoint.com/v1/url?u=http://pldserver1.biochem.queensu.ca/~rlc&k=7DHVT22D9IhC0F3WohFMBA%3D%3D%0A&r=1ciN0EuZ9XNq3lPnYtgkI5sKPXgKVaywidBN0C981SQ%3D%0A&m=fr2bAoLQoVgp9h2t2fgBvfGVVX7oQ1g14g1AODFz%2FRg%3D%0A&s=aaad7877cf1640401ae708b7b5f5a2fbe03abec4d2f0ef509e7360c0017ee225

HPCC Systems Open Source Big Data Platform from LexisNexis Risk Solutions
Find What Matters Most in Your Big Data with HPCC Systems
Open Source. Fast. Scalable. Simple. Ideal for Dirty Data.
Leverages Graph Analysis for Fast Processing & Easy Data Exploration
PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net)
Info Page: https://urldefense.proofpoint.com/v1/url?u=https://lists.sourceforge.net/lists/listinfo/pymol-users&k=7DHVT22D9IhC0F3WohFMBA%3D%3D%0A&r=1ciN0EuZ9XNq3lPnYtgkI5sKPXgKVaywidBN0C981SQ%3D%0A&m=fr2bAoLQoVgp9h2t2fgBvfGVVX7oQ1g14g1AODFz%2FRg%3D%0A&s=6e6df3376d82f34b3bce9c1de38053ec6052ce7313087062131127d0c0c03fb7
Archives: https://urldefense.proofpoint.com/v1/url?u=http://www.mail-archive.com/pymol-users%40lists.sourceforge.net&k=7DHVT22D9IhC0F3WohFMBA%3D%3D%0A&r=1ciN0EuZ9XNq3lPnYtgkI5sKPXgKVaywidBN0C981SQ%3D%0A&m=fr2bAoLQoVgp9h2t2fgBvfGVVX7oQ1g14g1AODFz%2FRg%3D%0A&s=f7df11447d13070db8093ed0604c19654bebcf07d28d46919253043bb5dbe80e

HPCC Systems Open Source Big Data Platform from LexisNexis Risk Solutions
Find What Matters Most in Your Big Data with HPCC Systems
Open Source. Fast. Scalable. Simple. Ideal for Dirty Data.
Leverages Graph Analysis for Fast Processing & Easy Data Exploration