Re: [PyMOL] Error: unknown type
Re: [PyMOL] Error: unknown type From: Justin Lecher j.lec...@fz... - 2009-05-12 17:34 Attachments: signature.asc I've updated it on the Wiki. So anyone likes to try git and update the repo? -- Justin Lecher Institute for Neuroscience and Biophysics INB 2 - Molecular Biophysics II Research centre Juelich GmbH, 52425 Juelich,Germany phone: +49 2461 61 5385 This actually highlights a weakness with trying to use git with the PyMOLWiki script library: updates. Until a script is written to automatically update git from the PyMOLWiki, I don't think git will help us too much--and in fact may cause confusion. The wiki already stores meta-information (comments, tags, see also's, etc) along with the code and it does have, albeit rather non-specific, versioning built in. So, summarizing: I think it's a great idea, but it will require effort on someone's part before this'll become widely used for the wiki. Thanks, -- Jason -- Jason Vertrees, PhD Boston U. -- jas...@bu.edu Dartmouth -- j...@cs.dartmouth.edu -- The NEW KODAK i700 Series Scanners deliver under ANY circumstances! Your production scanning environment may not be a perfect world - but thanks to Kodak, there's a perfect scanner to get the job done! With the NEW KODAK i700 Series Scanner you'll get full speed at 300 dpi even with all image processing features enabled. http://p.sf.net/sfu/kodak-com ___ PyMOL-users mailing list PyMOL-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/pymol-users
[PyMOL] create double bonds in small molecules
Hi, I've been trying to get PyMOL to display a double bond at the position of the vinyl in the attached, small-moleculePDB for some time. The PDB was generated by converting a smiles representation of isopentenly diphosphate (obtained from PubChem) using Corina. The number of attached atoms at the vinyl group is correct, but PyMOL doesn't display the double bond. Cycling the bond valence produces a single-bond version (with added protons), but stops there - it won't cycle through triple, double, single. Downloaded a PDB of fumarate that does display double bonds in response to Set Valence - so, my version of PyMOL (1.1beta2, Vista environment) seems fine. Thoughts? Thanks, TomBEGIN:VCARD VERSION:2.1 N:Leyh;Thomas;S.;Ph.D FN:Thomas S. Leyh ORG:AECOM;Biochemistry TEL;WORK;VOICE:718-430-2857 TEL;WORK;FAX:718-430-8565 ADR;WORK;ENCODING=QUOTED-PRINTABLE:;;Rm. 305 Forchh. Bldg.=0D=0A1300 Morris Park Ave.;Bronx;NY;10461 LABEL;WORK;ENCODING=QUOTED-PRINTABLE:Rm. 305 Forchh. Bldg.=0D=0A1300 Morris Park Ave.=0D=0ABronx, NY 10461 EMAIL;PREF;INTERNET:l...@aecom.yu.edu REV:20090514T171123Z END:VCARD isopentenly diphosphate.pse Description: Binary data -- The NEW KODAK i700 Series Scanners deliver under ANY circumstances! Your production scanning environment may not be a perfect world - but thanks to Kodak, there's a perfect scanner to get the job done! With the NEW KODAK i700 Series Scanner you'll get full speed at 300 dpi even with all image processing features enabled. http://p.sf.net/sfu/kodak-com___ PyMOL-users mailing list PyMOL-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/pymol-users
Re: [PyMOL] create double bonds in small molecules
Tom, set valence edit_mode Ctrl-right-click on the bond Ctrl-W seems to do the trick. Perhaps there's a problem with the version of PyMOL you're using? Cheers, Warren From: Thomas S. Leyh, Ph. D. [mailto:l...@aecom.yu.edu] Sent: Thursday, May 14, 2009 10:13 AM To: pymol-users@lists.sourceforge.net Subject: [PyMOL] create double bonds in small molecules Hi, I've been trying to get PyMOL to display a double bond at the position of the vinyl in the attached, small-moleculePDB for some time. The PDB was generated by converting a smiles representation of isopentenly diphosphate (obtained from PubChem) using Corina. The number of attached atoms at the vinyl group is correct, but PyMOL doesn't display the double bond. Cycling the bond valence produces a single-bond version (with added protons), but stops there - it won't cycle through triple, double, single. Downloaded a PDB of fumarate that does display double bonds in response to Set Valence - so, my version of PyMOL (1.1beta2, Vista environment) seems fine. Thoughts? Thanks, Tom -- The NEW KODAK i700 Series Scanners deliver under ANY circumstances! Your production scanning environment may not be a perfect world - but thanks to Kodak, there's a perfect scanner to get the job done! With the NEW KODAK i700 Series Scanner you'll get full speed at 300 dpi even with all image processing features enabled. http://p.sf.net/sfu/kodak-com___ PyMOL-users mailing list PyMOL-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/pymol-users
[PyMOL] POVRAY Usage
Hi All, While ray tracing a scene with 10 x-large proteins in grid mode at 3600, 3600 (width, height) I ran out of RAM (2 GB). I tried it again by writing everything into a script and using pymol -qc which still ran out of memory. I read somewhere that POVRAY is less of a memory hog so I installed the latest version and simply modified my script to ray 3600, 3600, renderer=1 to use POVRAY. Everything went smoothly but I noticed that the image generated from POVRAY looked different than the native ray traced structure using PyMOL's ray tracer (simply invoking ray without dimensions in PyMOL). Specifically, the light reflections appeared to be dulled in POVRAY and spheres that were further away from the camera view are not distinguishable. I've posted a comparison on the PyMOLWiki: http://www.pymolwiki.org/index.php/Povray_vs._pymol Firstly, I apologize as I am completely new to the world of POVRAY and I just assumed that the image produced from either method would give identical/close results but I much prefer the look of the PyMOL ray-tracer. Is there an easy way to set everything up the same way as the PyMOL ray-tracer but for POVRAY? Thank you for your time. Sean _ Find info faster and easier with Internet Explorer 8. http://go.microsoft.com/?linkid=9655583-- The NEW KODAK i700 Series Scanners deliver under ANY circumstances! Your production scanning environment may not be a perfect world - but thanks to Kodak, there's a perfect scanner to get the job done! With the NEW KODAK i700 Series Scanner you'll get full speed at 300 dpi even with all image processing features enabled. http://p.sf.net/sfu/kodak-com___ PyMOL-users mailing list PyMOL-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/pymol-users
Re: [PyMOL] POVRAY Usage
Hi Sean,
Unfortunately, getting a good image through POV-Ray requires editing
the POV-Ray file. You can write the scene to disk with the following
commands
pov=open(protein.pov,w)
pov.write(cmd.get_povray()[0])
pov.write(#include \povray.inc\)
pov.close()
open(povray.inc,w).write(cmd.get_povray()[1])
Then, take your favorite editor (under windows, you can use the
POV-Ray editor) and make some changes:
1. There's a line starting with #defaults. Remove that and replace it with:
#default {
finish {
ambient .15
diffuse .5
specular 1
roughness .001
reflection { .5 metallic } // Remove this line for less
glossyness and faster tracing
}
}
2. There's a light statement, which says:
light_source{4000.0001,4000.0001,9960. rgb1.0,1.0,1.0}.
Replace it with:
light_source
{
20,10,0
rgb 2
area_light 5,5,0,5,5
adaptive 1
jitter
}
This usually works for me :)
Note that the trace may now take some time. Remove the metallic
reflection for faster tracing.
I hope it helps. POV-Ray is cool, but rather complicated.
Cheers,
Tsjerk
On Thu, May 14, 2009 at 10:21 PM, Sean Law magic...@hotmail.com wrote:
Hi All,
While ray tracing a scene with 10 x-large proteins in grid mode at 3600, 3600
(width, height) I ran out of RAM (2 GB). I tried it again by writing
everything into a script and using pymol -qc which still ran out of memory.
I read somewhere that POVRAY is less of a memory hog so I installed the
latest version and simply modified my script to ray 3600, 3600, renderer=1
to use POVRAY. Everything went smoothly but I noticed that the image
generated from POVRAY looked different than the native ray traced structure
using PyMOL's ray tracer (simply invoking ray without dimensions in
PyMOL). Specifically, the light reflections appeared to be dulled in POVRAY
and spheres that were further away from the camera view are not
distinguishable. I've posted a comparison on the PyMOLWiki:
http://www.pymolwiki.org/index.php/Povray_vs._pymol
Firstly, I apologize as I am completely new to the world of POVRAY and I just
assumed that the image produced from either method would give identical/close
results but I much prefer the look of the PyMOL ray-tracer. Is there an easy
way to set everything up the same way as the PyMOL ray-tracer but for
POVRAY? Thank you for your time.
Sean
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Biomolecular NMR, Bijvoet Center
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3584 CH Utrecht
The Netherlands
P: +31-30-2539931
F: +31-30-2537623
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production scanning environment may not be a perfect world - but thanks to
Kodak, there's a perfect scanner to get the job done! With the NEW KODAK i700
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Re: [PyMOL] POVRAY Usage
Hi Sean,
Sorry about that. Tried from the top of my head and the evening had
past too far for that already. These vectors define the directions to
distribute the lights - you basically create an area of light sources.
So you need to set two vectors:
area_light 5,0,0,0,5,0,5,5
This will generate 25 lights in a five by five array perpendicular to
the Pymol viewing axis (which is always along z).
Cheers,
Tsjerk
On Thu, May 14, 2009 at 11:21 PM, Sean Law magic...@hotmail.com wrote:
Tsjerk,
Thanks for the quick response. I noticed that after area_light there
should be two axis vectors (according to the povray website) but you've only
specified one. Should I just repeat the same axis twice?
Sean
Date: Thu, 14 May 2009 22:47:54 +0200
Subject: Re: [PyMOL] POVRAY Usage
From: tsje...@gmail.com
To: magic...@hotmail.com
CC: pymol-users@lists.sourceforge.net
Hi Sean,
Unfortunately, getting a good image through POV-Ray requires editing
the POV-Ray file. You can write the scene to disk with the following
commands
pov=open(protein.pov,w)
pov.write(cmd.get_povray()[0])
pov.write(#include \povray.inc\)
pov.close()
open(povray.inc,w).write(cmd.get_povray()[1])
Then, take your favorite editor (under windows, you can use the
POV-Ray editor) and make some changes:
1. There's a line starting with #defaults. Remove that and replace it
with:
#default {
finish {
ambient .15
diffuse .5
specular 1
roughness .001
reflection { .5 metallic } // Remove this line for less
glossyness and faster tracing
}
}
2. There's a light statement, which says:
light_source{4000.0001,4000.0001,9960. rgb1.0,1.0,1.0}.
Replace it with:
light_source
{
20,10,0
rgb 2
area_light 5,5,0,5,5
adaptive 1
jitter
}
This usually works for me :)
Note that the trace may now take some time. Remove the metallic
reflection for faster tracing.
I hope it helps. POV-Ray is cool, but rather complicated.
Cheers,
Tsjerk
On Thu, May 14, 2009 at 10:21 PM, Sean Law magic...@hotmail.com wrote:
Hi All,
While ray tracing a scene with 10 x-large proteins in grid mode at 3600,
3600 (width, height) I ran out of RAM (2 GB). I tried it again by writing
everything into a script and using pymol -qc which still ran out of memory.
I read somewhere that POVRAY is less of a memory hog so I installed the
latest version and simply modified my script to ray 3600, 3600,
renderer=1
to use POVRAY. Everything went smoothly but I noticed that the image
generated from POVRAY looked different than the native ray traced structure
using PyMOL's ray tracer (simply invoking ray without dimensions in
PyMOL). Specifically, the light reflections appeared to be dulled in
POVRAY
and spheres that were further away from the camera view are not
distinguishable. I've posted a comparison on the PyMOLWiki:
http://www.pymolwiki.org/index.php/Povray_vs._pymol
Firstly, I apologize as I am completely new to the world of POVRAY and I
just assumed that the image produced from either method would give
identical/close results but I much prefer the look of the PyMOL ray-tracer.
Is there an easy way to set everything up the same way as the PyMOL
ray-tracer but for POVRAY? Thank you for your time.
Sean
Help keep personal info safe. Get Internet Explorer 8 today!
--
The NEW KODAK i700 Series Scanners deliver under ANY circumstances! Your
production scanning environment may not be a perfect world - but thanks
to
Kodak, there's a perfect scanner to get the job done! With the NEW KODAK
i700
Series Scanner you'll get full speed at 300 dpi even with all image
processing features enabled. http://p.sf.net/sfu/kodak-com
___
PyMOL-users mailing list
PyMOL-users@lists.sourceforge.net
https://lists.sourceforge.net/lists/listinfo/pymol-users
--
Tsjerk A. Wassenaar, Ph.D.
Junior UD (post-doc)
Biomolecular NMR, Bijvoet Center
Utrecht University
Padualaan 8
3584 CH Utrecht
The Netherlands
P: +31-30-2539931
F: +31-30-2537623
Internet Explorer 8 makes surfing easier. Get it now!
--
Tsjerk A. Wassenaar, Ph.D.
Junior UD (post-doc)
Biomolecular NMR, Bijvoet Center
Utrecht University
Padualaan 8
3584 CH Utrecht
The Netherlands
P: +31-30-2539931
F: +31-30-2537623
--
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