pymol-users Mailing List for PyMOL Molecular Graphics System

Dear Authors/Researchers

We are pleased to announce a call for papers for the new thematic issue on
*'*Peptide Science at the Chemistry Biology Interface*'* published by Current
Protein & Peptide Science
<" rel="nofollow">http://benthamscience.com/journal/index.php?journalID=cpps#top> (Impact
Factor: 2.326).

*Guest edited by Prof. Diwan S. Rawat,  Dr. Prija Ponnan *, this thematic
issue will publish review articles with emphasis on the frontiers of
peptide chemistry and biology covering contemporary and emerging
applications of peptide science involving topics such as *de novo* design
of peptide and peptide mimetic engineered with predictable structure and
function with better precision for targeted application; advances in cyclic
and macrocyclic peptide discovery; post-translationally modified peptide
and peptide-oligonucleotide conjugates intervening in biological processes,
controlling macromolecular assembly and binding; peptides as catalysts and
a basis for new biomaterials; discovery and manoeuvring of bioactive
natural peptides; using ligation approaches and amide bond formation in
peptide chemistry. Special attention will be given to the topics including
the application of peptide science in signal transduction; peptide-membrane
interactions; peptides as diagnostics; pharmaceuticals, biomaterials for
peptide delivery; peptides as imaging agents and peptide nano materials.

We welcome the submission of high-quality review articles to the thematic
issue of Current Protein & Peptide Science
<" rel="nofollow">http://benthamscience.com/journal/index.php?journalID=cpps#top> that
discuss research in the field of peptide science covering recent advances
in the field from the leading laboratories from different regions/countries
of the world and including future perspectives. Original papers, research
articles and letter articles/short communications are not considered for
publication in Current Protein & Peptide Science.
*The submission deadline is December 31, 2014.*


Guide to authors and other details are available on the Journal’s
website Current
Protein & Peptide Science
<." rel="nofollow">http://benthamscience.com/journal/index.php?journalID=cpps#top>.


Please note that all the submitted proposals will be peer reviewed prior to
any decision on acceptance for publication.

Interested Authors/ Researcher, please submit preliminary Abstract
containing a list of names and affiliations of contributing authors, titles
of proposed articles at pri...@gm....


*We would also appreciate if you could kindly circulate the information to
colleagues and other contacts in the field.*


Kind regards,

*Prof. Diwan S. Rawat and Dr. Prija Ponnan*

Guest Editors *Current Protein & Peptide Science*
<" rel="nofollow">http://benthamscience.com/journal/index.php?journalID=cpps#top>

Hi Jordan,

if you save the session file with "psw" extension, it becomes a "PyMOL Show File" which is opened in presentation mode, that's full screen without any controls.

Cheers,
  Thomas

On 18 Jun 2014, at 23:33, J.R. W <jwi...@gm...> wrote:
> Hi,
> 
> What I’d like to do is set_grid_mode_1, ray trace, and then output a png in batch mode (-c)
> 
> 
> However if you code this in the .pml:
> 
> set_grid_mode, 1
> set grid_slot, 2, object2
> set grid_slot, 1, object1
> 
> viewport 1000,1000 #not sure how to get fullscreen this maybe OS specific
> 
> ray 1000,1000
> png somepic.png
> cmd.save("lookatthis.pse”)
> 
> Grid mode does not show up in the picture and the viewport in the session is still the default window size. However, grid mode does work in the session. 
> 
> So my question(s) are this:
> 
> 1. Can you use grid mode in batch mode scripts to output an image?
> 2. Can you encode a full screen GUI in the pymol session so when you open up the session, it is full screen?
> 
> Using MacPyMOL latest release, can switch to X11 if necessary.
> 
> Thanks so much!
> 
> Jordan

-- 
Thomas Holder
PyMOL Developer
Schrödinger, Inc.

Hi Christian,

cartoon_side_chain_helper was implemented as an atom-level-setting in the latest Incentive PyMOL version. In older versions and in the current open-source, the setting is object-level. However, if you create a separate object like you said, it should work with these versions too. Just make sure you hide cartoon or unset the cartoon_side_chain_helper setting for that new object. Example:

PyMOL> fetch 1ubq, async=0
PyMOL> as cartoon
PyMOL> show sticks
PyMOL> set cartoon_side_chain_helper
PyMOL> create mygly, resi 35
PyMOL> as sticks, mygly
PyMOL> orient mygly

Cheers,
  Thomas

On 23 Jun 2014, at 14:13, Christian Roth <chr...@bb...> wrote:

> Hi there,
> 
> I used the side chain helper option to create a binding site in the 
> protein. However I want include a glycine, which doesn't show up. Even 
> when I create an extra object with the glycine and an neighbouring 
> residue I didn't get the carbonyl oxygen atom of glycine and I don't 
> want to switch of the side chain helper function for all residues.
> Is there a way to get that done without switching the helper function 
> completely off?
> 
> Thanks in advance for your help
> 
> Christian

-- 
Thomas Holder
PyMOL Developer
Schrödinger, Inc.

Hej,

I'm not sure about the side chain helper options, but you can always
selectively show displays.
You could try something like:

show_as cartoon, object
show sticks, sele and not name N+C+O

or:

show_as cartoon, object
show sticks, sele
hide sticks, name N+C+O

Either option should show the cartoon plus non-main chain atoms.

Hope that works,

/Andreas




On Mon, Jun 23, 2014 at 8:13 PM, Christian Roth <
chr...@bb...> wrote:

> Hi there,
>
> I used the side chain helper option to create a binding site in the
> protein. However I want include a glycine, which doesn't show up. Even
> when I create an extra object with the glycine and an neighbouring
> residue I didn't get the carbonyl oxygen atom of glycine and I don't
> want to switch of the side chain helper function for all residues.
> Is there a way to get that done without switching the helper function
> completely off?
>
> Thanks in advance for your help
>
> Christian
>
>
>
> ------------------------------------------------------------------------------
> 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
> http://p.sf.net/sfu/hpccsystems
> _______________________________________________
> PyMOL-users mailing list (PyM...@li...)
> Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users
> Archives: http://www.mail-archive.com/pym...@li...
>

Hi there,

I used the side chain helper option to create a binding site in the 
protein. However I want include a glycine, which doesn't show up. Even 
when I create an extra object with the glycine and an neighbouring 
residue I didn't get the carbonyl oxygen atom of glycine and I don't 
want to switch of the side chain helper function for all residues.
Is there a way to get that done without switching the helper function 
completely off?

Thanks in advance for your help

Christian

Hi Suzanne,

Everything should look and act exactly like it has in the past, including
the address.

Cheers,

-- Jason

--
Jason Vertrees, PhD
(e) Jas...@gm...
(o) +1 (603) 374-7120


On Fri, Jun 20, 2014 at 10:18 AM, Lapolla, Suzanne M (HSC) <
suz...@ou...> wrote:

>  Great! Thank you Microlytic! I assume that the PyMol wiki site will
> still have the same web address?
>  ------------------------------
> *From:* Jason Vertrees [jas...@gm...]
>
> *Sent:* Friday, June 20, 2014 8:00 AM
> *To:* pymol-users
> *Cc:* Melanie Adams-Cioaba
> *Subject:* [PyMOL] PyMOLWiki Update
>
>   Greetings,
>
>  It is my pleasure to let you know that Microlytic
> <," rel="nofollow">https://urldefense.proofpoint.com/v1/url?u=http://www.microlytic.com/&k=7DHVT22D9IhC0F3WohFMBA%3D%3D%0A&r=1ciN0EuZ9XNq3lPnYtgkI5sKPXgKVaywidBN0C981SQ%3D%0A&m=LCsIIUrfD4RcV5Fb7TWTnwdu4fFSpJmF7mTJQLv8%2BNI%3D%0A&s=c5f009784fbe8b4462388f99a44f3232d828141afea37db017b8d2ba026b9f3d>,
> a company that makes tools for crystallographers, has graciously offered to
> host the PyMOLWiki. The wiki has been successfully transferred and is
> serving. (The search and the port :8888 problems have been fixed. Please
> let me know if you find any other problems.)
>
>  Please join me in thanking Microlytic
> <" rel="nofollow">https://urldefense.proofpoint.com/v1/url?u=http://Melanie%2520Adams-Cioaba%2520%26lt%3Bmac%40microlytic.com%26gt%3B&k=7DHVT22D9IhC0F3WohFMBA%3D%3D%0A&r=1ciN0EuZ9XNq3lPnYtgkI5sKPXgKVaywidBN0C981SQ%3D%0A&m=LCsIIUrfD4RcV5Fb7TWTnwdu4fFSpJmF7mTJQLv8%2BNI%3D%0A&s=b2e04adca315e082abf51a6d98450782b86b9d5347605cd10510bdb863aa2146>
> for helping serve the PyMOL community.
>
>  Cheers,
>
>  -- Jason
>
>  --
> Jason Vertrees, PhD
> (e) Jas...@gm...
> (o) +1 (603) 374-7120
>

Great! Thank you Microlytic! I assume that the PyMol wiki site will still have the same web address?
________________________________
From: Jason Vertrees [jas...@gm...]
Sent: Friday, June 20, 2014 8:00 AM
To: pymol-users
Cc: Melanie Adams-Cioaba
Subject: [PyMOL] PyMOLWiki Update

Greetings,

It is my pleasure to let you know that Microlytic<," rel="nofollow">https://urldefense.proofpoint.com/v1/url?u=http://www.microlytic.com/&k=7DHVT22D9IhC0F3WohFMBA%3D%3D%0A&r=1ciN0EuZ9XNq3lPnYtgkI5sKPXgKVaywidBN0C981SQ%3D%0A&m=LCsIIUrfD4RcV5Fb7TWTnwdu4fFSpJmF7mTJQLv8%2BNI%3D%0A&s=c5f009784fbe8b4462388f99a44f3232d828141afea37db017b8d2ba026b9f3d>, a company that makes tools for crystallographers, has graciously offered to host the PyMOLWiki. The wiki has been successfully transferred and is serving. (The search and the port :8888 problems have been fixed. Please let me know if you find any other problems.)

Please join me in thanking Microlytic<" rel="nofollow">https://urldefense.proofpoint.com/v1/url?u=http://Melanie%2520Adams-Cioaba%2520%26lt%3Bmac%40microlytic.com%26gt%3B&k=7DHVT22D9IhC0F3WohFMBA%3D%3D%0A&r=1ciN0EuZ9XNq3lPnYtgkI5sKPXgKVaywidBN0C981SQ%3D%0A&m=LCsIIUrfD4RcV5Fb7TWTnwdu4fFSpJmF7mTJQLv8%2BNI%3D%0A&s=b2e04adca315e082abf51a6d98450782b86b9d5347605cd10510bdb863aa2146> for helping serve the PyMOL community.

Cheers,

-- Jason

--
Jason Vertrees, PhD
(e) Jas...@gm...<mailto:Jas...@gm...>
(o) +1 (603) 374-7120<tel:%2B1%20%28603%29%20374-7120>

Greetings,

It is my pleasure to let you know that Microlytic
<," rel="nofollow">http://www.microlytic.com/>, a company that makes tools for
crystallographers, has graciously offered to host the PyMOLWiki. The wiki
has been successfully transferred and is serving. (The search and the port
:8888 problems have been fixed. Please let me know if you find any other
problems.)

Please join me in thanking Microlytic <http://Melanie Adams-Cioaba
<ma...@mi...>> for helping serve the PyMOL community.

Cheers,

-- Jason

--
Jason Vertrees, PhD
(e) Jas...@gm...
(o) +1 (603) 374-7120

Hej,

I haven't tested, but the grid_mode should work, all you need to do is
correct the underscore typo:
set grid_mode, 1 # without _
set grid_slot, 2, object2
set grid_slot, 1, object1

Picture size and quality is not controlled by viewport unless you are
making a movie, in that case set viewport, ray_trace_frames and
movie_quality:
cmd.viewport(800,600)
cmd.set('ray_trace_frames',1)
cmd.set('movie_quality',100)
#Then use either:
cmd.mpng('example')
#or
cmd.movie.produce('example.mpg',mode='ray', preserve=0, quality=100)

I your case, however, a single image is best made using png:
e.g.

cmd.png('example.png', '15cm', '10cm', dpi=300, ray=1)

this will give you a 15x10 cm image at 300 dpi, regardless of viewport.
http://www.pymolwiki.org/index.php/Png

About starting in fullscreen:
using the command line option '-e' should make pymol start in fullscreen
this will probably not work with '-c', but you can open your script from
another shortcut.
http://www.pymolwiki.org/index.php/Command_Line_Options

Hope this helps,

/Andreas





On Thu, Jun 19, 2014 at 5:33 AM, J.R. W <jwi...@gm...> wrote:

> Hi,
>
> What I’d like to do is set_grid_mode_1, ray trace, and then output a png
> in batch mode (-c)
>
>
> However if you code this in the .pml:
>
> set_grid_mode, 1
> set grid_slot, 2, object2
> set grid_slot, 1, object1
>
> viewport 1000,1000 #not sure how to get fullscreen this maybe OS specific
>
> ray 1000,1000
> png somepic.png
> cmd.save("lookatthis.pse”)
>
> Grid mode* does not* show up in the picture and the viewport in the
> session is still the default window size. However, grid mode *does* work
> in the session.
>
> So my question(s) are this:
>
> 1. Can you use grid mode in batch mode scripts to output an image?
> 2. Can you encode a full screen GUI in the pymol session so when you open
> up the session, it is full screen?
>
> Using MacPyMOL latest release, can switch to X11 if necessary.
>
> Thanks so much!
>
> Jordan
>
>
>
>
> ------------------------------------------------------------------------------
> 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
> http://p.sf.net/sfu/hpccsystems
> _______________________________________________
> PyMOL-users mailing list (PyM...@li...)
> Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users
> Archives: http://www.mail-archive.com/pym...@li...
>

Hi,

What I’d like to do is set_grid_mode_1, ray trace, and then output a png in batch mode (-c)


However if you code this in the .pml:

set_grid_mode, 1
set grid_slot, 2, object2
set grid_slot, 1, object1

viewport 1000,1000 #not sure how to get fullscreen this maybe OS specific

ray 1000,1000
png somepic.png
cmd.save("lookatthis.pse”)

Grid mode does not show up in the picture and the viewport in the session is still the default window size. However, grid mode does work in the session. 

So my question(s) are this:

1. Can you use grid mode in batch mode scripts to output an image?
2. Can you encode a full screen GUI in the pymol session so when you open up the session, it is full screen?

Using MacPyMOL latest release, can switch to X11 if necessary.

Thanks so much!

Jordan

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 [Jar...@ny...]
Sent: Tuesday, June 17, 2014 5:54 PM
To: Lapolla, Suzanne M (HSC)
Cc: pym...@li...
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) <suz...@ou...<mailto: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 " rel="nofollow">http://www.pymolwiki.org/index.php/Measure_Distance<https://urldefense.proofpoint.com/v1/url?u=http://www.pymolwiki.org/index.php/Measure_Distance&k=7DHVT22D9IhC0F3WohFMBA%3D%3D%0A&r=1ciN0EuZ9XNq3lPnYtgkI5sKPXgKVaywidBN0C981SQ%3D%0A&m=HgvRHXkBNYGOysfvJcLojtIMeUFGMwyeOeg9H0RbBr0%3D%0A&s=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 [rob...@qu...<mailto:rob...@qu...>]
Sent: Monday, June 09, 2014 10:04 AM
To: pym...@li...<mailto: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...<mailto: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...<mailto: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...<mailto: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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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) <suz...@ou...<mailto: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...<mailto:rob...@qu...>]
Sent: Monday, June 09, 2014 10:04 AM
To: pym...@li...<mailto: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...<mailto: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...<mailto: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...<mailto: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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Ah I see--I will try and let you know how it works. Thanks again!
________________________________
From: Andreas Warnecke [4nd...@gm...]
Sent: Tuesday, June 17, 2014 2:18 PM
To: Lapolla, Suzanne M (HSC)
Cc: Robert Campbell; pym...@li...
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 <4nd...@gm...<mailto: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...<mailto: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 " rel="nofollow">http://www.pymolwiki.org/index.php/Measure_Distance<https://urldefense.proofpoint.com/v1/url?u=http://www.pymolwiki.org/index.php/Measure_Distance&k=7DHVT22D9IhC0F3WohFMBA%3D%3D%0A&r=1ciN0EuZ9XNq3lPnYtgkI5sKPXgKVaywidBN0C981SQ%3D%0A&m=EqubiL9cuYdYV13TK4bGte5vmf3Plq1xmWomVmdYlKU%3D%0A&s=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 [rob...@qu...<mailto:rob...@qu...>]
Sent: Monday, June 09, 2014 10:04 AM
To: pym...@li...<mailto: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...<mailto: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...<mailto: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<tel:613-533-6821>
<rob...@qu...<mailto: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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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
>>
>>
>> ------------------------------------------------------------------------------
>> 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%0A&r=1ciN0EuZ9XNq3lPnYtgkI5sKPXgKVaywidBN0C981SQ%3D%0A&m=fr2bAoLQoVgp9h2t2fgBvfGVVX7oQ1g14g1AODFz%2FRg%3D%0A&s=dabd029c6435c0bbe92d916555213bd7ccbd3d4ac6dcf2de28cf19c428ff0eed
>> _______________________________________________
>> PyMOL-users mailing list (PyM...@li...)
>> 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
>> http://p.sf.net/sfu/hpccsystems
>> _______________________________________________
>> PyMOL-users mailing list (PyM...@li...)
>> Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users
>> Archives: http://www.mail-archive.com/pym...@li...
>>
>
>

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
>
>
> ------------------------------------------------------------------------------
> 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%0A&r=1ciN0EuZ9XNq3lPnYtgkI5sKPXgKVaywidBN0C981SQ%3D%0A&m=fr2bAoLQoVgp9h2t2fgBvfGVVX7oQ1g14g1AODFz%2FRg%3D%0A&s=dabd029c6435c0bbe92d916555213bd7ccbd3d4ac6dcf2de28cf19c428ff0eed
> _______________________________________________
> PyMOL-users mailing list (PyM...@li...)
> 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
> http://p.sf.net/sfu/hpccsystems
> _______________________________________________
> PyMOL-users mailing list (PyM...@li...)
> Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users
> Archives: http://www.mail-archive.com/pym...@li...
>

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

------------------------------------------------------------------------------
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%0A&r=1ciN0EuZ9XNq3lPnYtgkI5sKPXgKVaywidBN0C981SQ%3D%0A&m=fr2bAoLQoVgp9h2t2fgBvfGVVX7oQ1g14g1AODFz%2FRg%3D%0A&s=dabd029c6435c0bbe92d916555213bd7ccbd3d4ac6dcf2de28cf19c428ff0eed
_______________________________________________
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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

THANK YOU, that was it!

On Jun 16, 2014, at 5:22 PM, Sampson, Jared <Jar...@ny...> wrote:

> set cartoon_ring_color, blue, my_selection

H. Adam Steinberg
7904 Bowman Rd
Lodi, WI 53555
608/592-2366

Hi H. Adam -

Try the cartoon_ring_color setting.  You can do this per-selection as well.

set cartoon_ring_color, blue, my_selection

Hope that helps!

Cheers,
Jared

--
Jared Sampson
Xiangpeng Kong Lab
NYU Langone Medical Center
http://kong.med.nyu.edu/






On Jun 16, 2014, at 4:57 PM, H. Adam Steinberg <h.a...@gm...<mailto:h.a...@gm...>> wrote:

Hi All,

Somehow I have turned on or adjusted a setting and cannot figure out what it is or how to turn it off.

All of the rings in my nucleic acid structures are filled (and that is okay) but they are all filled with green! They are not filled with the same color as the rest of the base.

Can anyone help?

Sample image attached…

<green ring.jpg>

H. Adam Steinberg
7904 Bowman Rd
Lodi, WI 53555
608/592-2366

------------------------------------------------------------------------------
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
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Hi All,

Somehow I have turned on or adjusted a setting and cannot figure out what it is or how to turn it off.

All of the rings in my nucleic acid structures are filled (and that is okay) but they are all filled with green! They are not filled with the same color as the rest of the base.

Can anyone help?

Sample image attached…



H. Adam Steinberg
7904 Bowman Rd
Lodi, WI 53555
608/592-2366

Impressive, how did you figure this out?

Martin




On 12.06.14 23:18, Shiven Shandilya wrote:
> Hi Martin,
>
> I guess you can do this using modified GLSL shaders …
>
> Two examples I posted on the PyMOL wiki a while ago:
> http://www.pymolwiki.org:8888/index.php/GLSL_Shaders
>
> Best,
> Shiven
>
>
> On Jun 12, 2014, at 5:10 PM, Martin Hediger <ma...@bl... 
> <mailto:ma...@bl...>> wrote:
>
>> Hi all
>>
>> I wonder if it's possible to have something like ray_trace_mode, 2 (i.e.
>> black and white with outlines) but in the interactive view. Also, is it
>> possible to have part of the structure in color (say some active site
>> amino acids) and the rest in black and white?
>>
>> Thanks for help
>> Martin
>>
>> ------------------------------------------------------------------------------
>> 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
>> http://p.sf.net/sfu/hpccsystems
>> _______________________________________________
>> PyMOL-users mailing list (PyM...@li... 
>> <mailto:PyM...@li...>)
>> Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users
>> Archives: http://www.mail-archive.com/pym...@li...
>

-- 
Dr. Martin R. Hediger
Schaffhauserstrasse 104
8057 Zürich

Hi Martin,

I guess you can do this using modified GLSL shaders …

Two examples I posted on the PyMOL wiki a while ago:
http://www.pymolwiki.org:8888/index.php/GLSL_Shaders

Best,
Shiven


On Jun 12, 2014, at 5:10 PM, Martin Hediger <ma...@bl...> wrote:

> Hi all
> 
> I wonder if it's possible to have something like ray_trace_mode, 2 (i.e. 
> black and white with outlines) but in the interactive view. Also, is it 
> possible to have part of the structure in color (say some active site 
> amino acids) and the rest in black and white?
> 
> Thanks for help
> Martin
> 
> ------------------------------------------------------------------------------
> 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
> http://p.sf.net/sfu/hpccsystems
> _______________________________________________
> PyMOL-users mailing list (PyM...@li...)
> Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users
> Archives: http://www.mail-archive.com/pym...@li...

Hi all

I wonder if it's possible to have something like ray_trace_mode, 2 (i.e. 
black and white with outlines) but in the interactive view. Also, is it 
possible to have part of the structure in color (say some active site 
amino acids) and the rest in black and white?

Thanks for help
Martin

Hello,

I've been developing a PyMOL plugin using Tkinter, and encountered an issue
with the slider (scale) widget and an associated variable leading way to a
segfault as the slider value is changed. Below is a segment of the code
I've minimized as much as reasonable while still giving the error. The time
it takes to segfault varies, but I haven't seen it take more than a few
seconds of moving the slider.

Python Code:

import Tkinter

import pymol

def __init_plugin__(self=None):

        pymol.plugins.addmenuitem('segfaulter', main)

def main():

        root = Tkinter.Toplevel(pymol.plugins.get_tk_root())

        var = Tkinter.DoubleVar()

        slider = Tkinter.Scale(root,variable=var)

        slider.grid()

        varCallback = var.trace_variable('w', lambda x,y,z:function(var))

def function(var):

        print(var)

Any ideas on what might be going on, or suggestions to eliminate the error?
Thank you very much!

Best Regards,
Berk

Hi Gian,

yes, the from_numpy method is new in PyMOL 1.7. But the underlying import functionality is not new, so you could basically copy the code from that method and create a valid brick instance yourself. Have a look at:

https://sourceforge.net/p/pymol/code/HEAD/tree/trunk/pymol/modules/chempy/brick.py#l28

Cheers,
 Thomas

On 12 Jun 2014, at 16:40, Gianluca Santoni <gia...@ib...> wrote:

> Hi everyone,
> I was following this instructions to load a nparray as a map, but I get 
> the error:
> class Brick has no attribute 'from_numpy'
> 
> Is it a new feature in chempy, or am I missing something?
> Cheers,
> Gian
> 
> On 2/3/14 3:01 AM, Thomas Holder wrote:
>> Hi Esben,
>> 
>> On 02 Feb 2014, at 12:27, Esben Jannik Bjerrum <esb...@ro...> wrote:
>>> ... I also found a nifty example from brick01.py in the examples directory, but to get it to render in linux, numpy needs to be compiled into PyMOL, does this also hold for Your solution Thomas?
>> 
>> yes, PyMOL needs to be compiled with numpy for chempy.brick support. Incentive PyMOL ships with numpy support, and open-source PyMOL has numpy support if it can "import numpy" during compilation.
>> 
>> Cheers,
>>   Thomas
> 
> -- 
> Gianluca Santoni,
> Dynamop Group
> Institut de Biologie Structurale
> 6 rue Jules Horowitz							
> 38027 Grenoble Cedex 1						
> France

-- 
Thomas Holder
PyMOL Developer
Schrödinger, Inc.

Hi everyone,
I was following this instructions to load a nparray as a map, but I get 
the error:
class Brick has no attribute 'from_numpy'

Is it a new feature in chempy, or am I missing something?
Cheers,
Gian


On 2/3/14 3:01 AM, Thomas Holder wrote:
> Hi Esben,
>
> On 02 Feb 2014, at 12:27, Esben Jannik Bjerrum <esb...@ro...> wrote:
>> ... I also found a nifty example from brick01.py in the examples directory, but to get it to render in linux, numpy needs to be compiled into PyMOL, does this also hold for Your solution Thomas?
>
> yes, PyMOL needs to be compiled with numpy for chempy.brick support. Incentive PyMOL ships with numpy support, and open-source PyMOL has numpy support if it can "import numpy" during compilation.
>
> Cheers,
>    Thomas
>


-- 
Gianluca Santoni,
Dynamop Group
Institut de Biologie Structurale
6 rue Jules Horowitz							
38027 Grenoble Cedex 1						
France	
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