pymol-users — Collaborative support and tips for PyMOL users

[PyMOL] how to extract corresponding residue pairs after alignment ?

[Indraneel M. <ind...@sm...>]

Hi,

Is there any way to extract corresponding residue/atom pairs after alignment?
eg. the atoms that are used to create the cgo when "object" option is
specified. (I guess this is probably in op1.ai1VLA and op2.ai1VLA in
layer3/Executive.c ?)

Thanks in advance,
Indraneel

-- 
http://prodata.swmed.edu

Re: [PyMOL] Re: New spectral color pallette

[Robert C. <rl...@po...>]

Alexander,

* Ale...@bc... wrote:
> >
> > I would like to color my protein according to B-factor with a self-defined
> > spectral palette (In this case I have put sequence conservation into the
> > Bfactor this column). I found that
> >         spectrum b, blue_white_red, minimum=0, maximum=100
> > would do part of the job with a predefined pallette
> >
> > - I could not find out how to define my own new color palette like
> > "white_red".
> > - Is there a way to "visualize" the color palettes before applying it to
> > an object?
> >

* Seth Harris <se...@gm...> [2005-12-31 09:54] wrote:
> This is more half an answer than the real deal, but when I had the same
> issue I opted for the quick work around of setting the range from -100 to
> 100 for the blue-white-red palette which effectively made 0-100 correspond
> to white to red only since there were no negative B factors/conservation
> scores.
> e.g.
> spectrum b, blue_white_red, minimum=-100, maximum=100
> 
> I am curious for better answers, as you are, but haven't delved into the
> code to look for it myself, either. But perhaps this or some fine tuning of
> the range or other pre-defined palettes will get done what you desire.

I have a script, color_b.py, available on my website that allows one
to colour based on the value of the B-factor or occupancy columns. It
currently has the following colour gradients:

      'bgr': blue -> green   -> red
      'rgb': red  -> green   -> blue
      'bwr': blue -> white   -> red
      'rwb': red  -> white   -> blue
      'bmr': blue -> magenta -> red
      'rmb': red  -> magenta -> blue
      'rw' : red -> white
      'wr' : white -> red
      'gw' : green -> white
      'wg' : white -> green
      'bw' : blue -> white
      'wb' : white -> blue
      'gy' : green -> yellow
      'yg' : yellow -> green
      'gray' : black -> white
      'reversegray' : white -> black

It isn't too difficult to add more gradients by following the recipes in
the "make_gradient" function in that script. It is also possible to set
the minimum and maximum values to tune the exact gradient limits as well
as to set the saturation and brightness (value) of the colours, via the
command options.

Hope this helps.

Cheers,
Rob
-- 
Robert L. Campbell, Ph.D.                         <rl...@po...>
Senior Research Associate                            phone: 613-533-6821
Dept. of Biochemistry, Queen's University,             fax: 613-533-2497
Kingston, ON K7L 3N6  Canada       http://adelie.biochem.queensu.ca/~rlc
    PGP Fingerprint: 9B49 3D3F A489 05DC B35C  8E33 F238 A8F5 F635 C0E2

Re: [PyMOL] mesh for compound molecule

[Joel T. <joe...@ot...>]

Hi Lena,

I know it might not be the best way but you can change the hetatm name 
to atom and then create a separate object in pymol. or read in a 
separate file with the above change

J

le...@gm... wrote:

>Hello PyMOL-users,
>
>I was wandering how to show the mesh on the compound molecule (i.e. other
>structures that amino acids inside of a protein).  Any visualization similar
>to electron density would be also useful.
>
>Thanks!!
>lena
>
>  
>

-- 
Joel Tyndall, PhD

Lecturer
National School of Pharmacy
University of Otago
PO Box 913 Dunedin
New Zealand                     

Pukenga
Te Kura Taiwhanga Putaiao
Te Whare Wananga o Otago
Pouaka Poutapeta 913 Otepoti
Aotearoa

Ph / Waea               +64 3 4797293 
Fax / Waeawhakaahua     +64 3 4797034

Re: [PyMOL] Ray, png

[<Mat...@im...>]

pym...@li... wrote on 01/03/2006 05:32:38 PM:

> Hi,
> On the subject of larger image sizes, I had a question a while back;
> I'd like to know if it's been addressed or anyone has a quick(er)
workaround-
> Basically, is there in inverse to the viewport command?  i.e., if I
> manually resize the Pymol window to fit around the molecule I'm
> displaying, how can I get the relative dimensions of the new window?
> These dimensions are needed for the Ray command to keep proper
> perspective.  What I've done in the past is save a small image of
> what's displayed in the window, used a graphics program to determine
> the x & y dimensions, and then used these to generate a high-
> resolution ray traced image with the same x/y ratio.
> I figure I'm missing something.
>
> Regards,
>

Hi David -

I usually just write a temporary png image to get the viewport dimensions,
i.e.

PyMOL>png junk.png
 ScenePNG: wrote 640x480 pixel image to file "junk.png".

As long as you haven't just executed a raytracing, the png dimensions are
the viewport dimensions.

- Matt

--
Matthew Franklin                     phone:(917)606-4116
Senior Scientist, ImClone Systems      fax:(212)645-2054
180 Varick Street, 6th floor
New York, NY 10014


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[PyMOL] mesh for compound molecule

[<le...@gm...>]

Hello PyMOL-users,

I was wandering how to show the mesh on the compound molecule (i.e. other
structures that amino acids inside of a protein).  Any visualization similar
to electron density would be also useful.

Thanks!!
lena

-- 
Lust, ein paar Euro nebenbei zu verdienen? Ohne Kosten, ohne Risiko!
Satte Provisionen für GMX Partner: http://www.gmx.net/de/go/partner

[PyMOL] Feedback on New Macs w/ Stereo3D

[Warren D. <wa...@de...>]

MacPyMOL Users,

If you've recently bought a Stereo 3D-equipped G5 Single/Dual/Quad for
running MacPyMOL and other scientific codes, please let me know -- I'd
like some candid real-world feedback on how well these systems are
performing...

Cheers,
Warren

--
Warren L. DeLano, Ph.D.                    =20
Principal Scientist

. DeLano Scientific LLC =20
. 400 Oyster Point Blvd., Suite 213          =20
. South San Francisco, CA 94080 USA  =20
. Biz:(650)-872-0942  Tech:(650)-872-0834    =20
. Fax:(650)-872-0273  Cell:(650)-346-1154
. mailto:wa...@de...     =20

RE: [PyMOL] Drawing surfaces in pymol?

[Terry J. <tc...@ca...>]

| This isn't really something PyMOL was designed to do.  You could construct
| such a surface using Python CGO facility, but that means doing the
| tesselation, surface normal calculation, and any culling yourself.

Thanks. Is this what you do already in pymol to make surfaces that envelop
points?

Thanks too for the ray answer.

Terry

[PyMOL] Drawing surfaces in pymol?

[Terry J. <tc...@ca...>]

I've been using PyQt/Coin/SoQt/pivy to draw surfaces using SoNurbsSurface.

I'm wondering if something like this is possible in pymol?

I.e., I specify a set of points in 3D space and use pymol to lay an
interpolated surface over them. I don't want the surface to fully envelop
the points in the way that pymol can show surfaces around a series of
points.  If this is possible, can I also trim such a surface (in Coin this
is done using an SoNurbsCurve)?

I've put a image showing the sort of thing I'm already generating at
http://jones.tc/other/surface.png (Ignore the grid at bottom).

Thanks for any help or suggestions.
Terry

[PyMOL] ray

[Terry J. <tc...@ca...>]

Here's another question about ray. At what level in pymol is it
implemented? Is it part of what's provided by OpenGL, or done at some
higher/other level?

Terry

RE: [PyMOL] Ray, png

[Warren D. <wa...@de...>]

David,

In recent builds, you don't need to specify both dimensions for the ray
command -- just give it height or width and it will compute the other
based on the current aspect ratio.

Regardless, to get the current window, here is one way:

print cmd.get_session()['main']

Cheers,
Warren

--
Warren L. DeLano, Ph.D.                    =20
Principal Scientist

. DeLano Scientific LLC =20
. 400 Oyster Point Blvd., Suite 213          =20
. South San Francisco, CA 94080 USA  =20
. Biz:(650)-872-0942  Tech:(650)-872-0834    =20
. Fax:(650)-872-0273  Cell:(650)-346-1154
. mailto:wa...@de...     =20
=20

> -----Original Message-----
> From: pym...@li...=20
> [mailto:pym...@li...] On Behalf Of=20
> David A. Horita
> Sent: Tuesday, January 03, 2006 2:39 PM
> To: pym...@li...
> Subject: [PyMOL] Ray, png
>=20
> Hi,
> On the subject of larger image sizes, I had a question a=20
> while back; I'd like to know if it's been addressed or anyone=20
> has a quick(er) workaround- Basically, is there in inverse to=20
> the viewport command?  i.e., if I manually resize the Pymol=20
> window to fit around the molecule I'm displaying, how can I=20
> get the relative dimensions of the new window?  These=20
> dimensions are needed for the Ray command to keep proper=20
> perspective.  What I've done in the past is save a small=20
> image of what's displayed in the window, used a graphics=20
> program to determine the x & y dimensions, and then used=20
> these to generate a high-resolution ray traced image with the=20
> same x/y ratio.
> I figure I'm missing something.
> =20
> Regards,
> =20
> =20
> -----------------------------
> David A. Horita, Ph.D.
> Department of Biochemistry
> Wake Forest University School of Medicine Winston-Salem, NC 27157-1016
> Tel: 336 713-4194
> Fax: 336 716-7671
> email:  dh...@wf...
> web:  http://www1.wfubmc.edu/biochem/faculty/Horita.htm=20
> <http://www1.wfubmc.edu/biochem/faculty/Horita.htm/>=20
> =20
>=20

[PyMOL] Ray, png

[David A. H. <dh...@wf...>]

Hi,
On the subject of larger image sizes, I had a question a while back; I'd
like to know if it's been addressed or anyone has a quick(er)
workaround-
Basically, is there in inverse to the viewport command?  i.e., if I
manually resize the Pymol window to fit around the molecule I'm
displaying, how can I get the relative dimensions of the new window?
These dimensions are needed for the Ray command to keep proper
perspective.  What I've done in the past is save a small image of what's
displayed in the window, used a graphics program to determine the x & y
dimensions, and then used these to generate a high-resolution ray traced
image with the same x/y ratio.
I figure I'm missing something.
=20
Regards,
=20
=20
-----------------------------=20
David A. Horita, Ph.D.
Department of Biochemistry
Wake Forest University School of Medicine
Winston-Salem, NC 27157-1016=20
Tel: 336 713-4194
Fax: 336 716-7671=20
email:  dh...@wf...
web:  http://www1.wfubmc.edu/biochem/faculty/Horita.htm
<http://www1.wfubmc.edu/biochem/faculty/Horita.htm/>=20
=20

Re: [PyMOL] Saving Images

[Joel T. <joe...@ot...>]

If you would like appropriately scaled images then you can set up your 
viewer to the appropriate dimensions eg for a square

viewport 700,700

or rectangle

viewport 800,400

If using a square I then use

ray 1800,1800

this ray traces an image larger than your pymol window and allows you to 
save it. This will help with higher resolution images. Newer versions 
show a preview. You canuop the resolution by increasing the ray pixels

Hope this helps

J

Peter Adrian Meyer wrote:

>>Hi everyone,
>>Each time I try to save images, Pymol writes 640x480
>>pixel image to the file. I wonder if there is a way to
>>save images (png format) other than 640X480 pixel that
>>is default.
>>Any help will be appreciated.
>>Thanks.
>>    
>>
>
>Images are saved as either the size of the viewer window, or the ray
>traced size.  The easiest way to get a larger image is to maximize the
>viewer window, and then save.  To get an arbritray size, use the
>ray-tracer (ray 1024,768 ; png BigImage.png).
>
>Pete
>
>
>
>Pete Meyer
>Fu Lab
>BMCB grad student
>Cornell University
>
>
>
>-------------------------------------------------------
>This SF.net email is sponsored by: Splunk Inc. Do you grep through log files
>for problems?  Stop!  Download the new AJAX search engine that makes
>searching your log files as easy as surfing the  web.  DOWNLOAD SPLUNK!
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>
>  
>

-- 
Joel Tyndall, PhD

Lecturer
National School of Pharmacy
University of Otago
PO Box 913 Dunedin
New Zealand                     

Pukenga
Te Kura Taiwhanga Putaiao
Te Whare Wananga o Otago
Pouaka Poutapeta 913 Otepoti
Aotearoa

Ph / Waea               +64 3 4797293 
Fax / Waeawhakaahua     +64 3 4797034

[PyMOL] Bond lengths

[Andy C. <And...@br...>]

Dear People,

I was wondering if if people could recommend
	1) a way of generating all bond lengths and bond angles for a molecule
automatically(atm I'm using the measurement wizard)
	2) a method for increasing the size of the font produced by the
measurement wizard

If I have missed something previously posted,  can you please refer me
to a valid url.
Thanks for your help
Andy
-- 

If you're not part of the solution, you're part of the precipitate.

[PyMOL] Re: New spectral color pallette

[Seth H. <se...@gm...>]

This is more half an answer than the real deal, but when I had the same
issue I opted for the quick work around of setting the range from -100 to
100 for the blue-white-red palette which effectively made 0-100 correspond
to white to red only since there were no negative B factors/conservation
scores.
e.g.
spectrum b, blue_white_red, minimum=3D-100, maximum=3D100

I am curious for better answers, as you are, but haven't delved into the
code to look for it myself, either. But perhaps this or some fine tuning of
the range or other pre-defined palettes will get done what you desire.

Cheers,
Seth



> Message: 1
> From: Ale...@bc...
> To: pym...@li...
> Date: Fri, 30 Dec 2005 10:24:10 +0100
> Subject: [PyMOL] new spectral color palette
>
> This message is in MIME format. Since your mail reader does not understan=
d
> this format, some or all of this message may not be legible.
>
> ------_=3D_NextPart_001_01C60D22.CA0F1A47
> Content-Type: text/plain
> Content-Transfer-Encoding: 7bit
>
> Hi
>
> I would like to color my protein according to B-factor with a self-define=
d
> spectral palette (In this case I have put sequence conservation into the
> Bfactor this column). I found that
>         spectrum b, blue_white_red, minimum=3D0, maximum=3D100
> would do part of the job with a predefined pallette
>
> - I could not find out how to define my own new color palette like
> "white_red".
> - Is there a way to "visualize" the color palettes before applying it to
> an
> object?
>
> Thanks for any help.
>
> alex
>
>
>
> >  Dr. Alexander Pautsch
> >  Protein Crystallography /Structural Research
> >  Boehringer Ingelheim Pharma GmbH & Co. KG Deutschland
> >  Birkendorferstrasse 65
> >  88400 BIBERACH, Germany
> >  tel. +49 - (0)7351 - 54 4683
> >  fax. +49 - (0)7351 - 83 4683
> >  email ale...@bc...
> >
> >
> >
>
>
>

[PyMOL] new spectral color palette

[<Ale...@bc...>]

Hi

I would like to color my protein according to B-factor with a self-defined
spectral palette (In this case I have put sequence conservation into the
Bfactor this column). I found that 
	spectrum b, blue_white_red, minimum=0, maximum=100 
would do part of the job with a predefined pallette

- I could not find out how to define my own new color palette like
"white_red".
- Is there a way to "visualize" the color palettes before applying it to an
object?

Thanks for any help.

alex



>  Dr. Alexander Pautsch
>  Protein Crystallography /Structural Research 
>  Boehringer Ingelheim Pharma GmbH & Co. KG Deutschland 
>  Birkendorferstrasse 65
>  88400 BIBERACH, Germany 
>  tel. +49 - (0)7351 - 54 4683 
>  fax. +49 - (0)7351 - 83 4683
>  email ale...@bc...
> 
> 
> 

[PyMOL] Lighting models b29 vs. b31

[Mark A S. <sa...@um...>]

I know that the lighting model for ray tracing in beta 31 is  
different than beta 29.  But ray tracing of surfaces looks  
significantly better in beta 29.   Beta 29 is brighter and the  
specular highlights are more subtle (less contrast).  Any suggestions  
how to emulate beta29 appearance in beta31?

Thanks,
Mark

_________________________________
Mark A. Saper, Ph.D.
Associate Professor of Biological Chemistry
Biophysics Research Division, University of Michigan
Chemistry Building Room 3040
930 N University Ave
Ann Arbor MI 48109-1055 U.S.A.

sa...@um...        (734) 764-3353        fax (734) 764-3323
http://www.biochem.med.umich.edu/biochem/research/profiles/saper.html

Re: [PyMOL] Saving Images

[Peter A. M. <pa...@co...>]

> Hi everyone,
> Each time I try to save images, Pymol writes 640x480
> pixel image to the file. I wonder if there is a way to
> save images (png format) other than 640X480 pixel that
> is default.
> Any help will be appreciated.
> Thanks.

Images are saved as either the size of the viewer window, or the ray
traced size.  The easiest way to get a larger image is to maximize the
viewer window, and then save.  To get an arbritray size, use the
ray-tracer (ray 1024,768 ; png BigImage.png).

Pete



Pete Meyer
Fu Lab
BMCB grad student
Cornell University

[PyMOL] Saving Images

[Michael M. <dwa...@ya...>]

Hi everyone,
Each time I try to save images, Pymol writes 640x480
pixel image to the file. I wonder if there is a way to
save images (png format) other than 640X480 pixel that
is default.
Any help will be appreciated.
Thanks.


	
		
__________________________________ 
Yahoo! for Good - Make a difference this year. 
http://brand.yahoo.com/cybergivingweek2005/

[PyMOL] APBS windows version

[kmk <km...@gi...>]

Hi, all

Recently, I obtained APBS windows version and than installed. It works well.

Is it possible use in Pymol windows version? 


I found one error message 
ObjectMapLoadDXFile-Error: Unable to open file!


Sincerely yours,

Kim, Mun-kyoung

Protein Structure and Function Laboratory
Department of Life Science
Gwangju Institute of Science and Technology (GIST)
1 Oryong - Dong, Puk-Gu, Gwangju, Korea, 500-712
Tel: +82-062-970-2549
Fax: +82-062-970-2484
Lab http://xray.gist.ac.kr 

[PyMOL] internal GUI: letters vanish on window enlargement

[bgbg bg <bg...@gm...>]

Hello, I am experiencing a pretty annoying problem: when enlarging the PyMo=
l
window, the letters inside the
internal gui slowly disappear.
I've done several screenshots that demonstrate the problem:
the full view:
 http://dl13.rapidshare.de/files/10017550/146939542/vanish.png
focus on the disappearing letters:
http://dl12.rapidshare.de/files/10017564/146941916/vanish_enlarged.png

If the images are not available, try the following links, scroll down and
click "Free download":
http://rapidshare.de/files/10017550/vanish.png<http://rapidshare.de/files/1=
0017550/vanish.png.html>
http://rapidshare.de/files/10017564/vanish_enlarged.png

Is this a known bug or is it a problem with my setup?

[PyMOL] Active site pockets determination

[Oded K. <od...@in...>]

Hi,
I trying to assign and visualize the different pockets in protease 
active site (S3, S2, S1, S1',S2', S3') and then to compare these pockets 
in different proteases using the same calculation/approach.  What is the 
best tool/way for doing this with pymol?
Thanks,
Oded

RE: [PyMOL] Video adapter recommendations?

[Warren D. <wa...@de...>]

Pretty much any card in that price range from ATI or nVidia will work
great.=20

Cheers,
Warren

--
Warren L. DeLano, Ph.D.                    =20
Principal Scientist

. DeLano Scientific LLC =20
. 400 Oyster Point Blvd., Suite 213          =20
. South San Francisco, CA 94080 USA  =20
. Biz:(650)-872-0942  Tech:(650)-872-0834    =20
. Fax:(650)-872-0273  Cell:(650)-346-1154
. mailto:wa...@de...     =20
=20

> -----Original Message-----
> From: pym...@li...=20
> [mailto:pym...@li...] On Behalf Of=20
> Vsevolod (Simon) Ilyushchenko
> Sent: Thursday, December 15, 2005 11:31 AM
> To: pym...@li...
> Subject: [PyMOL] Video adapter recommendations?
>=20
> Hi,
>=20
> What recent video cards do you recommend for running Pymol on Windows?
> We can spend around $500 on a card, but we'd like to make=20
> sure that it's worth buying.
>=20
> Thanks,
> Simon
> --=20
>=20
> Simon (Vsevolod ILyushchenko)   si...@cs...
> 				http://www.simonf.com
>=20
> "Think like a man of action, act like a man of thought."
>=20
> 		         Henri Bergson
>=20
>=20
> -------------------------------------------------------
> This SF.net email is sponsored by: Splunk Inc. Do you grep=20
> through log files for problems?  Stop!  Download the new AJAX=20
> search engine that makes searching your log files as easy as=20
> surfing the  web.  DOWNLOAD SPLUNK!
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> _______________________________________________
> PyMOL-users mailing list
> PyM...@li...
> https://lists.sourceforge.net/lists/listinfo/pymol-users
>=20
>=20
>=20
>=20

RE: [PyMOL] Surface representations

[Warren D. <wa...@de...>]

Greg,

alter all,vdw=3Dvdw-0.4
rebuild

Cheers,
Warren

--
Warren L. DeLano, Ph.D.                    =20
Principal Scientist

. DeLano Scientific LLC =20
. 400 Oyster Point Blvd., Suite 213          =20
. South San Francisco, CA 94080 USA  =20
. Biz:(650)-872-0942  Tech:(650)-872-0834    =20
. Fax:(650)-872-0273  Cell:(650)-346-1154
. mailto:wa...@de...     =20
=20

> -----Original Message-----
> From: pym...@li...=20
> [mailto:pym...@li...] On Behalf Of Greg C
> Sent: Thursday, December 22, 2005 12:10 PM
> To: pym...@li...
> Subject: [PyMOL] Surface representations
>=20
> Hi Pymolers,
>=20
> I am looking at a protein molecule in surface representation.=20
>  Is there a way to have the surface be "closer" to the=20
> atoms/sidechains, i.e. not as bulky?  This is just for=20
> illustration sake.
>=20
> Thanks!
> -Greg
>=20
>=20
>=20
>=20
> -------------------------------------------------------
> This SF.net email is sponsored by: Splunk Inc. Do you grep=20
> through log files for problems?  Stop!  Download the new AJAX=20
> search engine that makes searching your log files as easy as=20
> surfing the  web.  DOWNLOAD SPLUNK!
> http://ads.osdn.com/?ad_id=3D7637&alloc_id=3D16865&op=3Dclick
> _______________________________________________
> PyMOL-users mailing list
> PyM...@li...
> https://lists.sourceforge.net/lists/listinfo/pymol-users
>=20
>=20
>=20
>=20

[PyMOL] Surface representations

[Greg C <gre...@ho...>]

Hi Pymolers,

I am looking at a protein molecule in surface representation.  Is there a 
way to have the surface be "closer" to the atoms/sidechains, i.e. not as 
bulky?  This is just for illustration sake.

Thanks!
-Greg

Re: [PyMOL] MacPyMOL command entry

[gilleain t. <gil...@gm...>]

Hi,

I've noticed this too, it can be quite frustrating. Oddly, the histories fo=
r
the two windows (main, and command) seem to be different.

I have never managed to work out what the problem is, but I sometimes wonde=
r
if it is to do with whether a function returns a result or not? (Wild guess=
!
:)

gilleain

On 12/22/05, Mark A Saper <sa...@um...> wrote:
>
> Hi,
>
> Happy Holidays everyone.  This is actually a bug report for Warren.
> If you have time, could you work on the implementation of the command
> recall option (up and down arrow) in the command text input field in
> the OS X-specific part of the window.  It often forgets what the
> previous commands are.
>
> Many thanks,
> Mark
> _________________________________
> Mark A. Saper, Ph.D.
> Associate Professor of Biological Chemistry
> Associate Research Scientist in Biophysics
>
> Biophysics Research Division, University of Michigan
> Chemistry Building Room 3040
> 930 North University Ave
> Ann Arbor MI 48109-1055 U.S.A.
>
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