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Re: [PyMOL] command question RE printing out distances to text file
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From: Andreas W. <4nd...@gm...> - 2014-06-17 19:18:24
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One more addition to the reply:
I failed to notice that you are trying to input a range of residues '17-19'
Make sure to input single atom selections to get correct distances and not
an average:
A straightforward way to get that name is to click on the atom while in the
'editing mode' of pymol: pymol will print: "you clicked" followed by a name
that can be copy-pasted.
e.g. "You clicked /lys///LYS`2/CA -> (pk1)" can be used to copy-paste
/lys///LYS`2/CA
Another alternative is to use selections to identify one atom:
e.g.
cmd.distance('chain B and resi 297 and name CB','chain A and resi 17 and
name CB')
Then your example becomes:
from pymol import cmd
# open dist.txt for writing
f=open('distnew.txt','w')
# calculate the distance and store it in dst
dst1=cmd.distance('chain B and resi 297 and name CB','chain A and resi 17
and name CB')
dst2=cmd.distance('chain B and resi 297 and name CB','chain A and resi 18
and name CB')
dst3=cmd.distance('chain B and resi 297 and name CB','chain A and resi 19
and name CB')
# 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)
f.close()
Cheers,
Andreas
On Tue, Jun 17, 2014 at 8:45 PM, Andreas Warnecke <
4nd...@gm...> wrote:
> 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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>> 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
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