Thanks for your input Jared. I have not had a chance yet to try ANdrea's suggestions but will and will also try yours, and see what works best for me and get back to you and the forum--which has been so helpful! 

From: Sampson, Jared [Jared.Sampson@nyumc.org]
Sent: Tuesday, June 17, 2014 5:54 PM
To: Lapolla, Suzanne M (HSC)
Cc: pymol-users@lists.sourceforge.net
Subject: Re: [PyMOL] command question RE printing out distances to text file

Hi Suzanne - The reason you have been getting only one distance in your output file is that your script is opening the file in “write” mode:

f=open('distnew.txt','w')

This will overwrite the contents of distnew.txt each time the script is run.  If you want to keep all the distances without changing the rest of your script, you could open the file in “append” mode.  

f=open('distnew.txt',’a’)

This way, each line will just get added to the bottom of the script.  Keep in mind that if you want to start over with a new list of distances, you’ll need either to change the filename that gets opened (as you’ve done with “distnew.txt”) or delete the existing file.  For this reason, I would go with one of the other approaches mentioned by Andreas, or look into using a list to define the atoms to which you’d like to measure the distance from the first atom, and loop through that list.  Perhaps something like this (untested) bit of script would be useful, especially if you have many different atoms to check:


first_atom = 'B///297/cb'
second_atoms_list = ['A///17/cb', 'A///18/cb', 'A///19/cb']

with open("dist.txt", 'w') as f:
    for second_atom in second_atoms_list:
        f.write("%8.3f\n" % cmd.distance("tmp", first_atom, second_atom))


Good luck!

Cheers,
Jared

On Jun 17, 2014, at 2:21 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
f=open('distnew.txt','w')

# calculate the distance and store it in dst
dst=cmd.distance('tmp','B///297/cb','A///17-19/cb')

# write the formatted value of the distance (dst)
# to the output file
f.write("%8.3f\n"%dst)

# close the output file.
f.close()
________________________________________
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
directly.

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


Cheers,
Rob

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

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