Re: [PyMOL] command question RE printing out distances to text file
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.campb...@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.hol...@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_Distancek=7DHVT22D9IhC0F3WohFMBA%3D%3D%0Ar=1ciN0EuZ9XNq3lPnYtgkI5sKPXgKVaywidBN0C981SQ%3D%0Am=fr2bAoLQoVgp9h2t2fgBvfGVVX7oQ1g14g1AODFz%2FRg%3D%0As=921f4dfed39cd38f4ae7a70dfb937844d4e3faf1bc967c2f4d1f2944fa2ea31b
Cheers,
Thomas
On 06 Jun 2014, at 23:03, Lapolla, Suzanne M (HSC)
suzanne-lapo...@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.campb...@queensu.ca
https://urldefense.proofpoint.com/v1/url?u=http://pldserver1.biochem.queensu.ca/~rlck=7DHVT22D9IhC0F3WohFMBA%3D%3D%0Ar=1ciN0EuZ9XNq3lPnYtgkI5sKPXgKVaywidBN0C981SQ%3D%0Am=fr2bAoLQoVgp9h2t2fgBvfGVVX7oQ1g14g1AODFz%2FRg%3D%0As=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
https://urldefense.proofpoint.com/v1/url?u=http://www.hpccsystems.com/k=7DHVT22D9IhC0F3WohFMBA%3D%3D%0Ar=1ciN0EuZ9XNq3lPnYtgkI5sKPXgKVaywidBN0C981SQ%3D%0Am=fr2bAoLQoVgp9h2t2fgBvfGVVX7oQ1g14g1AODFz%2FRg%3D%0As=dabd029c6435c0bbe92d916555213bd7ccbd3d4ac6dcf2de28cf19c428ff0eed
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Re: [PyMOL] command question RE printing out distances to text file
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)
suzanne-lapo...@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.campb...@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.hol...@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_Distancek=7DHVT22D9IhC0F3WohFMBA%3D%3D%0Ar=1ciN0EuZ9XNq3lPnYtgkI5sKPXgKVaywidBN0C981SQ%3D%0Am=fr2bAoLQoVgp9h2t2fgBvfGVVX7oQ1g14g1AODFz%2FRg%3D%0As=921f4dfed39cd38f4ae7a70dfb937844d4e3faf1bc967c2f4d1f2944fa2ea31b
Cheers,
Thomas
On 06 Jun 2014, at 23:03, Lapolla, Suzanne M (HSC)
suzanne-lapo...@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.campb...@queensu.ca
https://urldefense.proofpoint.com/v1/url?u=http://pldserver1.biochem.queensu.ca/~rlck=7DHVT22D9IhC0F3WohFMBA%3D%3D%0Ar=1ciN0EuZ9XNq3lPnYtgkI5sKPXgKVaywidBN0C981SQ%3D%0Am=fr2bAoLQoVgp9h2t2fgBvfGVVX7oQ1g14g1AODFz%2FRg%3D%0As=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
https://urldefense.proofpoint.com/v1/url?u=http://www.hpccsystems.com/k=7DHVT22D9IhC0F3WohFMBA%3D%3D%0Ar=1ciN0EuZ9XNq3lPnYtgkI5sKPXgKVaywidBN0C981SQ%3D%0Am=fr2bAoLQoVgp9h2t2fgBvfGVVX7oQ1g14g1AODFz%2FRg%3D%0As=dabd029c6435c0bbe92d916555213bd7ccbd3d4ac6dcf2de28cf19c428ff0eed
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Re: [PyMOL] command question RE printing out distances to text file
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
4ndreas.warne...@gmail.com 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)
suzanne-lapo...@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.campb...@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.hol...@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_Distancek=7DHVT22D9IhC0F3WohFMBA%3D%3D%0Ar=1ciN0EuZ9XNq3lPnYtgkI5sKPXgKVaywidBN0C981SQ%3D%0Am=fr2bAoLQoVgp9h2t2fgBvfGVVX7oQ1g14g1AODFz%2FRg%3D%0As=921f4dfed39cd38f4ae7a70dfb937844d4e3faf1bc967c2f4d1f2944fa2ea31b
Cheers,
Thomas
On 06 Jun 2014, at 23:03, Lapolla, Suzanne M (HSC)
suzanne-lapo...@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
Re: [PyMOL] command question RE printing out distances to text file
Ah I see--I will try and let you know how it works. Thanks again!
From: Andreas Warnecke [4ndreas.warne...@gmail.com]
Sent: Tuesday, June 17, 2014 2:18 PM
To: Lapolla, Suzanne M (HSC)
Cc: Robert Campbell; pymol-users@lists.sourceforge.net
Subject: Re: [PyMOL] command question RE printing out distances to text file
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
4ndreas.warne...@gmail.commailto:4ndreas.warne...@gmail.com 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)
suzanne-lapo...@ouhsc.edumailto:suzanne-lapo...@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_Distancehttps://urldefense.proofpoint.com/v1/url?u=http://www.pymolwiki.org/index.php/Measure_Distancek=7DHVT22D9IhC0F3WohFMBA%3D%3D%0Ar=1ciN0EuZ9XNq3lPnYtgkI5sKPXgKVaywidBN0C981SQ%3D%0Am=EqubiL9cuYdYV13TK4bGte5vmf3Plq1xmWomVmdYlKU%3D%0As=992466ee53608d828281d0abbd95dc2742e6c75173eb93ae511f357e3225548b
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.campb...@queensu.camailto:robert.campb...@queensu.ca]
Sent: Monday, June 09, 2014 10:04 AM
To: pymol-users@lists.sourceforge.netmailto: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.hol...@schrodinger.commailto:thomas.hol...@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.
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-lapo...@ouhsc.edumailto:suzanne-lapo...@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.campb...@queensu.camailto:robert.campb...@queensu.ca]
Sent: Monday, June 09, 2014 10:04 AM
To: pymol-users@lists.sourceforge.netmailto: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.hol...@schrodinger.commailto:thomas.hol...@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_Distancek=7DHVT22D9IhC0F3WohFMBA%3D%3D%0Ar=1ciN0EuZ9XNq3lPnYtgkI5sKPXgKVaywidBN0C981SQ%3D%0Am=fr2bAoLQoVgp9h2t2fgBvfGVVX7oQ1g14g1AODFz%2FRg%3D%0As=921f4dfed39cd38f4ae7a70dfb937844d4e3faf1bc967c2f4d1f2944fa2ea31b
Cheers,
Thomas
On 06 Jun 2014, at 23:03, Lapolla, Suzanne M (HSC)
suzanne-lapo...@ouhsc.edumailto:suzanne-lapo...@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.campb...@queensu.camailto:robert.campb...@queensu.ca
https://urldefense.proofpoint.com/v1/url?u=http://pldserver1.biochem.queensu.ca/~rlck=7DHVT22D9IhC0F3WohFMBA%3D%3D%0Ar=1ciN0EuZ9XNq3lPnYtgkI5sKPXgKVaywidBN0C981SQ%3D%0Am=fr2bAoLQoVgp9h2t2fgBvfGVVX7oQ1g14g1AODFz%2FRg%3D%0As=aaad7877cf1640401ae708b7b5f5a2fbe03abec4d2f0ef509e7360c0017ee225
Re: [PyMOL] command question RE printing out distances to text file
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.samp...@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-lapo...@ouhsc.edumailto:suzanne-lapo...@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_Distancehttps://urldefense.proofpoint.com/v1/url?u=http://www.pymolwiki.org/index.php/Measure_Distancek=7DHVT22D9IhC0F3WohFMBA%3D%3D%0Ar=1ciN0EuZ9XNq3lPnYtgkI5sKPXgKVaywidBN0C981SQ%3D%0Am=HgvRHXkBNYGOysfvJcLojtIMeUFGMwyeOeg9H0RbBr0%3D%0As=439e1d97d8ba13b7f5cbabee32757f69dbeb6ec35476f43fd8eecc19d2e1539e
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.campb...@queensu.camailto:robert.campb...@queensu.ca]
Sent: Monday, June 09, 2014 10:04 AM
To: pymol-users@lists.sourceforge.netmailto: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.hol...@schrodinger.commailto:thomas.hol...@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_Distancek=7DHVT22D9IhC0F3WohFMBA%3D%3D%0Ar=1ciN0EuZ9XNq3lPnYtgkI5sKPXgKVaywidBN0C981SQ%3D%0Am=fr2bAoLQoVgp9h2t2fgBvfGVVX7oQ1g14g1AODFz%2FRg%3D%0As=921f4dfed39cd38f4ae7a70dfb937844d4e3faf1bc967c2f4d1f2944fa2ea31b
Cheers,
Thomas
On 06 Jun 2014, at 23:03, Lapolla, Suzanne M (HSC)
suzanne-lapo...@ouhsc.edumailto:suzanne-lapo...@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
