Re: [PyMOL] command question RE printing out distances to text file

[Andreas W. <4nd...@gm...>]

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
dst1=cmd.distance('tmp','B///297/cb','A///17-19/cb')
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
f.write("%8.3f\n"%dst1)
f.write("%8.3f\n"%dst2)
f.write("%8.3f\n"%dst3)

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

Cheers,

Andreas


On Tue, Jun 17, 2014 at 8:21 PM, Lapolla, Suzanne M (HSC) <
suz...@ou...> 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 [rob...@qu...]
> Sent: Monday, June 09, 2014 10:04 AM
> To: pym...@li...
> 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 <tho...@sc...> 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)
> > <suz...@ou...> 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
> <rob...@qu...>
> 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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