pymol-users Mailing List for PyMOL Molecular Graphics System

Hi Craig,

On Tue, 31 Aug 2010 09:29:44 -0500 Craig Smith <boi...@ma...> wrote:

> Hello,
> 
> Thanks for the prompt responses I received so far.  That really helped.
> But, set_color black changes the color globally.  Can I do this locally?
> For example, I'm highlighting two polypeptide chains one blue and one
> yellow.  The yellow labels are hard to see and I want to change them to
> black but the keep the blue chain labels blue.

Yes you can to this locally (at least by object). Simply add the object name
to the command. Say you have two objects called "object1" and "object2" and
you want to label all of the C-alpha carbons with the residue name and
number, you could do:

label name ca, "%s %s" % (resn,resi)

set label_color, black, object1
set label_color, blue, object2

Cheers,
Rob
-- 
Robert L. Campbell, Ph.D.
Senior Research Associate/Adjunct Assistant Professor 
Botterell Hall Rm 644
Department of Biochemistry, Queen's University, 
Kingston, ON K7L 3N6  Canada
Tel: 613-533-6821            Fax: 613-533-2497
<rob...@qu...>    http://pldserver1.biochem.queensu.ca/~rlc

Hello,

Thanks for the prompt responses I received so far.  That really helped.  But, set_color black changes the color globally.  Can I do this locally?  For example, I'm highlighting two polypeptide chains one blue and one yellow.  The yellow labels are hard to see and I want to change them to black but the keep the blue chain labels blue.

Craig

On Tue, Aug 31, 2010 at 6:31 AM, Craig Smith <boi...@ma...> wrote:
Hello,

I'm to make the color of my label different from the color of the residue.  For example, I have my carbons colored yellow but its label is hard to see and I want to change the color to black.  How do I do this?

Craig


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set label_color, black
can help you.
Abhi


On Tue, Aug 31, 2010 at 6:31 AM, Craig Smith <boi...@ma...> wrote:

> Hello,
>
> I'm to make the color of my label different from the color of the residue.
>  For example, I have my carbons colored yellow but its label is hard to see
> and I want to change the color to black.  How do I do this?
>
> Craig
>
>
>
> ------------------------------------------------------------------------------
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>
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Hello,

I'm to make the color of my label different from the color of the residue.  For example, I have my carbons colored yellow but its label is hard to see and I want to change the color to black.  How do I do this?

Craig

Hi Sebastien,

If you have multiple poses of the same molecule in your sdf file, you
can translate them into a multi-model PDB file, writing the score and
rmsd values to the bfactor and occupancy field. This you can then load
into pymol, allowing you to step through the poses. With the command
'spectrum' you can colour according to b-factor or occupancy, allowing
a quick judgment of the quality of a certain pose.
I'm not sure if it will also work that way if the sdf file contains
different molecules.

Hope it helps,

Tsjerk

On Mon, Aug 30, 2010 at 9:51 AM, Sebastian Kruggel
<kr...@ch...> wrote:
> dear all,
>
> i try to find a way of displaying data about molecules
> contained in a sdf file (score and rmsd values of docked
> poses) - at the best as labels.
>
> in the mailing list i only find information about displaying
> the title or splitting the sdf. i would like to keep the
> multimolecular character of the file (to go through the
> poses) but display the data of the sdf. is there any way to
> do this?
>
> thanks in advance,
> sebastian
>
>
>
>
> --
> Sebastian Kruggel
> Institut für Pharmazie
> Bundesstr. 45 | Raum 112 (406)
> D 20146 Hamburg
>
> Tel:   +49 (0)40 42838-3626 (-3484)
> mail:  kr...@ch...
> http://www.chemie.uni-hamburg.de/pha/phachem/lemcke/mitarbeiter.html
>
> ------------------------------------------------------------------------------
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> Archives: http://www.mail-archive.com/pym...@li...
>



-- 
Tsjerk A. Wassenaar, Ph.D.

post-doctoral researcher
Molecular Dynamics Group
Groningen Institute for Biomolecular Research and Biotechnology /
University of Groningen
The Netherlands

dear all,

i try to find a way of displaying data about molecules 
contained in a sdf file (score and rmsd values of docked 
poses) - at the best as labels.

in the mailing list i only find information about displaying 
the title or splitting the sdf. i would like to keep the 
multimolecular character of the file (to go through the 
poses) but display the data of the sdf. is there any way to 
do this?

thanks in advance,
sebastian




-- 
Sebastian Kruggel
Institut für Pharmazie
Bundesstr. 45 | Raum 112 (406)
D 20146 Hamburg

Tel:   +49 (0)40 42838-3626 (-3484)
mail:  kr...@ch...
http://www.chemie.uni-hamburg.de/pha/phachem/lemcke/mitarbeiter.html

Hi Vivek,

That's pretty odd.  I've never heard of that.  What's in your ~/.pymolrc file?

Cheers,

-- Jason

On Fri, Aug 27, 2010 at 2:59 PM, Vivek Ranjan <vr...@gm...> wrote:
> Hello,
>
> I ran a script in pymol "run axes.py" once. After killing pymol and
> restarting it, pymol always runs the script. Any reason for this
> behavior ?
>
> I was also wondering if there is a way to display just one axis in
> pymol without running a script ?
>
> --
> Thank you and Regards,
>
> Vivek Ranjan
>
> ------------------------------------------------------------------------------
> Sell apps to millions through the Intel(R) Atom(Tm) Developer Program
> Be part of this innovative community and reach millions of netbook users
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>



-- 
Jason Vertrees, PhD
PyMOL Product Manager
Schrodinger, LLC

(e) Jas...@sc...
(o) +1 (603) 374-7120

Hello,

I ran a script in pymol "run axes.py" once. After killing pymol and
restarting it, pymol always runs the script. Any reason for this
behavior ?

I was also wondering if there is a way to display just one axis in
pymol without running a script ?

-- 
Thank you and Regards,

Vivek Ranjan

Hi Dear Jason,

I have a problem to obtain the Axpymol plugin,  I have downloaded  the Pymol 1.2 
software from pymol.org/educational but without Axpymol. Is there an educational 
type of Axpmol for students to present the thesis with powerpoint. I would be 
thankful to answer me and  suggest any way to achieve that.

All the best,
Sima 


      

Hi Martin,

I can think of two ways to achieve this.  You can attempt to be tricky and add

  from pymol import stored
  stored.outFile = open("/my/myHbons.txt", 'w')

to your script and then inside the iterate commands instead of

  'print "%1s/%3s`%s/%-4s " % (chain, resn, resi, name),')

put

  'stored.outFile.write("%1s/%3s`%s/%-4s " % (chain, resn, resi, name)')


Or, second, you could just use "stored" to make a few lists to save
your data and then write those lists to disk:

from pymol import stored
stored.listA = []
>     for pairs in hb:
>         cmd.iterate("%s and index %s" % (pairs[0][0], pairs[0][1]),
>             'stored.listA.append( "%1s/%3s`%s/%-4s " % (chain, resn, resi, name)')
...
then after all your lists are created,

outFile = open("/tmp/myHbonds.txt", 'w')
for curLine in stored.listA:
  outFile.write(curLine + "\n")
outFile.close()

which should write to the file /tmp/myHbonds.txt with your data.

Cheers,

-- Jason


On Thu, Aug 26, 2010 at 11:07 AM, Martin Hediger <ma...@bl...> wrote:
>  Dear all
> I am using the script of Robert Campell to collect hydrogen bonds and
> the essential part looks like this:
>
> [collect pairs in hb by cmd.find_pairs]
>     for pairs in hb:
>         cmd.iterate("%s and index %s" % (pairs[0][0], pairs[0][1]),
>             'print "%1s/%3s`%s/%-4s " % (chain, resn, resi, name),')
>
>
>         cmd.iterate("%s and index %s" % (pairs[1][0],pairs[1][1]),
>                 'print "%1s/%3s`%s/%-4s " % (chain, resn, resi, name),')
>
>
>         print "%.2f" % cmd.distance(hb_list_name, "%s and index %s" %
>                 (pairs[0][0], pairs[0][1]), "%s and index %s" %
> (pairs[1][0],
>                     pairs[1][1]))
>
> This nicely lists three columns, where the interacting pairs are shown
> together with the length of the hydrogen bond.
> I have now started various unsuccessfull attempts to direct the output
> of 'cmd.iterate(...)' to a file which I would like to process further
> (sorting for largest change for two different configurations, etc.).
>
> How do I direct the output from iterate to a file?
>
> Suggestions would be appreciated.
> Martin
>
> ------------------------------------------------------------------------------
> Sell apps to millions through the Intel(R) Atom(Tm) Developer Program
> Be part of this innovative community and reach millions of netbook users
> worldwide. Take advantage of special opportunities to increase revenue and
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>



-- 
Jason Vertrees, PhD
PyMOL Product Manager
Schrodinger, LLC

(e) Jas...@sc...
(o) +1 (603) 374-7120

  Dear all
I am using the script of Robert Campell to collect hydrogen bonds and 
the essential part looks like this:

[collect pairs in hb by cmd.find_pairs]
     for pairs in hb:
         cmd.iterate("%s and index %s" % (pairs[0][0], pairs[0][1]),
             'print "%1s/%3s`%s/%-4s " % (chain, resn, resi, name),')


         cmd.iterate("%s and index %s" % (pairs[1][0],pairs[1][1]),
                 'print "%1s/%3s`%s/%-4s " % (chain, resn, resi, name),')


         print "%.2f" % cmd.distance(hb_list_name, "%s and index %s" %
                 (pairs[0][0], pairs[0][1]), "%s and index %s" % 
(pairs[1][0],
                     pairs[1][1]))

This nicely lists three columns, where the interacting pairs are shown 
together with the length of the hydrogen bond.
I have now started various unsuccessfull attempts to direct the output 
of 'cmd.iterate(...)' to a file which I would like to process further 
(sorting for largest change for two different configurations, etc.).

How do I direct the output from iterate to a file?

Suggestions would be appreciated.
Martin

Please remove my e-mail from your list.

Thank you.

Jae-Hong Lim

Hi Paul,

Free educational builds are still available.  I moved the link when I
reorganized the site.  Go here http://pymol.org/educational for more
info.

Cheers,

-- Jason

On Wed, Aug 25, 2010 at 8:53 AM, Paul Paukstelis
<sho...@gm...> wrote:
> I would be interested in using pymol in my class. Is there an
> educational build that students can download? All the links I found are
> dead. Thanks.
>
>
> --paul
>
> ------------------------------------------------------------------------------
> Sell apps to millions through the Intel(R) Atom(Tm) Developer Program
> Be part of this innovative community and reach millions of netbook users
> worldwide. Take advantage of special opportunities to increase revenue and
> speed time-to-market. Join now, and jumpstart your future.
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>



-- 
Jason Vertrees, PhD
PyMOL Product Manager
Schrodinger, LLC

(e) Jas...@sc...
(o) +1 (603) 374-7120

I would be interested in using pymol in my class. Is there an 
educational build that students can download? All the links I found are 
dead. Thanks.


--paul

Hi Martin,

to hide all carbon bound hydrogens, you can do it like this:

as sticks
hide sticks, (elem C extend 1) and (elem H)

Cheers,
  Thomas

On Wed, Aug 25, 2010 at 11:44 AM, Martin Hediger <ma...@bl...> wrote:
>  Hi all
> Is there a way to have the command "as sticks" show sticks and only
> polar hydrogens? Right now it shows all hydrogens and it would be nice
> if I could set it to leave out non polar hydrogens.
>
> Thanks for any suggestions.
>
> Martin

  Hi all
Is there a way to have the command "as sticks" show sticks and only 
polar hydrogens? Right now it shows all hydrogens and it would be nice 
if I could set it to leave out non polar hydrogens.

Thanks for any suggestions.

Martin

Oren,

Please see http://www.mail-archive.com/pym...@li.../msg07245.html.
 We recently had a discussion on this (I think Robert Campbell had
some wise words to say about this) but I cannot find the post.

So, the naming is:  prefixAAXXYYZZ, where PREFIX is your protein's
name (or specified prefix), AA is the number corresponding to the
symmetry operator (which matrix caused this translation/rotation), and
XX, YY and ZZ are labels indicating in which direction the new object
has been translated: -1 = down an axis; 0 no change; 1 = up the axis,
so you can get various combinations: XX=-10 or 01 for example.

Cheers,

-- Jason

On Mon, Aug 23, 2010 at 11:13 AM,  <ore...@po...> wrote:
> Hello
> I am trying to annotate the pymol symmetry coding (0100000) into
> symmetry operator (x,y,z)
> does anyone know how to do this?
>
> thanks
> oren yaniv
> prof. Felix Frolow laboratory
> biotechnology and molecular microbiology department
> tel aviv university
>
>
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-- 
Jason Vertrees, PhD
PyMOL Product Manager
Schrodinger, LLC

(e) Jas...@sc...
(o) +1 (603) 374-7120

Hi Chen,

What version of PyMOL are you using?  What machine and architecture?

If you send me a copy of your PyMOL session, I can take a look at it.

Cheers,

-- Jason

On Tue, Aug 24, 2010 at 9:08 AM, Chen Guttman <cgu...@gm...> wrote:
> Hey all,
> Following several rendering sessions, I've noticed that several setups &
> configurations that I've issued have been modified by the Ray command e.g.
> bond thickness, fogginess and depth of field control. For some reason, no
> matter what changes I am applying to the image, the rendition maintains the
> same appearance.
> Anyone has a clue how I progress from here?
> 10x,
> Chen
>
> ------------------------------------------------------------------------------
> Sell apps to millions through the Intel(R) Atom(Tm) Developer Program
> Be part of this innovative community and reach millions of netbook users
> worldwide. Take advantage of special opportunities to increase revenue and
> speed time-to-market. Join now, and jumpstart your future.
> http://p.sf.net/sfu/intel-atom-d2d
> _______________________________________________
> PyMOL-users mailing list (PyM...@li...)
> Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users
> Archives: http://www.mail-archive.com/pym...@li...
>



-- 
Jason Vertrees, PhD
PyMOL Product Manager
Schrodinger, LLC

(e) Jas...@sc...
(o) +1 (603) 374-7120

Hey all,
Following several rendering sessions, I've noticed that several setups &
configurations that I've issued have been modified by the Ray command e.g.
bond thickness, fogginess and depth of field control. For some reason, no
matter what changes I am applying to the image, the rendition maintains the
same appearance.
Anyone has a clue how I progress from here?
10x,
Chen

Hi,

Does anyone use the density map slider script developed by Gareth
Stockwell (http://www.ebi.ac.uk/~gareth/pymol/) ?

I have tried the script but ended with my PyMOL windows are freezing
(no response after executing "density_sliders").

My working environment:

1. OS: Windows Vista SP1
2. Cygwin, Python 2.6 with Pmw 1.3.2  installed
3. PyMOL open source revision 3915 and compiled in Cygwin.
4. Density map file is dx format. It can be loaded and displayed in
PyMOL without any problem.

Thanks in advance

Hung-Pin

Hello
I am trying to annotate the pymol symmetry coding (0100000) into  
symmetry operator (x,y,z)
does anyone know how to do this?

thanks
oren yaniv
prof. Felix Frolow laboratory
biotechnology and molecular microbiology department
tel aviv university

Hi Martin,

Great question--and a great, detailed way to ask the question, too.

I can think of two methods using PyMOL.  The first would be for PyMOL
subscribers or those who have FreeMOL with their PyMOL.  The second
uses PyMOL's native "sculpting".  This should make the unreasonable
reasonable, but of course has not been validated.  Use at your own
risk.

(0) Start each by selecting the atoms in which you're interested, so
that they're in the mouse selection, (sele).

# Method 1
# fix other atoms
flag fix, not sele

# clean up the selection
clean sele

# reset the fix flag
flag fix, (sele), clear



# Method 2: replace "target_obj" with name of the original protein
# create a temporary object on which to sculpt
create mod, (sele)

# turn on sculpting for this object
sculpt_activate mod

# sculpt a little
sculpt_iterate mod
sculpt_deactivate mod

# update the source object
update target_obj, mod

# remove mod
delete mod


Let me know how those work for you.

Cheers,

-- Jason


On Mon, Aug 23, 2010 at 8:20 AM, Martin Hediger <ma...@bl...> wrote:
>  Hi all
> Given this situation:
>
> Ser-O-H   NH-R2
>
> with the 'bond' and 'unbond' commands, I can form and cut a bond so that
> I get
>
> Ser-O H--NH-R2
>
> But this seems to have just a visual effect, meaning the coordinates of
> the proton do not change.
> I would like to know now if there is a smart way of adjusting the
> coordinates of the proton to reasonable (default) values. What in fact
> would be necessary is to just minimize the H-N part of the structure,
> everything else can stay as is.
> Is this by any chance possible with the sculpting functionality in
> PyMOL? Or is the only way to do this by manually adjusting the bond
> length within EDITING mode?
>
> Thanks a lot for any suggestions
> Martin
>
> ------------------------------------------------------------------------------
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>



-- 
Jason Vertrees, PhD
PyMOL Product Manager
Schrodinger, LLC

(e) Jas...@sc...
(o) +1 (603) 374-7120

  Hi all
Given this situation:

Ser-O-H   NH-R2

with the 'bond' and 'unbond' commands, I can form and cut a bond so that 
I get

Ser-O H--NH-R2

But this seems to have just a visual effect, meaning the coordinates of 
the proton do not change.
I would like to know now if there is a smart way of adjusting the 
coordinates of the proton to reasonable (default) values. What in fact 
would be necessary is to just minimize the H-N part of the structure, 
everything else can stay as is.
Is this by any chance possible with the sculpting functionality in 
PyMOL? Or is the only way to do this by manually adjusting the bond 
length within EDITING mode?

Thanks a lot for any suggestions
Martin

Thanks, Roger!  It's now fixed.

Cheers,

-- Jason

On Fri, Aug 20, 2010 at 2:43 PM, Roger Rowlett <rro...@co...> wrote:
> Jason,
>
> Thanks for the Endnote reference! I corrected a small formatting error in
> the author field which prevents it from displaying as "Schrodinger, L." in
> the citation instead of "Schrodinger, LLC". The Author field should be
> [Schrodinger,, LLC] and not [Schrodinger, LLC,] (minus the square brackets).
> Works in Endnote X2.
>
> Cheers.
>
>
> --
> ________________________________
> Roger S. Rowlett
> Professor
> Department of Chemistry
> Colgate University
> 13 Oak Drive
> Hamilton, NY 13346
>
> tel: (315)-228-7245
> ofc: (315)-228-7395
> fax: (315)-228-7935
> email: rro...@co...
>
>
> ------------------------------------------------------------------------------
> This SF.net email is sponsored by
>
> Make an app they can't live without
> Enter the BlackBerry Developer Challenge
> http://p.sf.net/sfu/RIM-dev2dev
> _______________________________________________
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> Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users
> Archives: http://www.mail-archive.com/pym...@li...
>



-- 
Jason Vertrees, PhD
PyMOL Product Manager
Schrodinger, LLC

(e) Jas...@sc...
(o) +1 (603) 374-7120

<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
<html>
  <head>

    <meta http-equiv="content-type" content="text/html; charset=ISO-8859-1">
  </head>
  <body bgcolor="#ffffff" text="#000000">
    <font face="Verdana">Jason,<br>
      <br>
      Thanks for the Endnote reference! I corrected a small formatting
      error in the author field which prevents it from displaying as
      "Schrodinger, L." in the citation instead of "Schrodinger, LLC".
      The Author field should be [Schrodinger,, LLC] and not
      [Schrodinger, LLC,] (minus the square brackets). Works in Endnote
      X2.<br>
      <br>
      Cheers.<br>
      <br>
      <br>
    </font>
    <div class="moz-signature">-- <br>
      <font face="Verdana">
        <hr>
        Roger S. Rowlett<br>
        Professor<br>
        Department of Chemistry<br>
        Colgate University<br>
        13 Oak Drive<br>
        Hamilton, NY 13346<br>
        <br>
        tel: (315)-228-7245<br>
        ofc: (315)-228-7395<br>
        fax: (315)-228-7935<br>
        email: <a class="moz-txt-link-abbreviated" href="mailto:rro...@co...">rro...@co...</a><br>
      </font>
    </div>
    <br>
  </body>
</html>