Re: [PyMOL] PyMOL-users Digest, Vol 45, Issue 9
Thank you Daniel, I finally found the Autodock tool path in Mac however, i got another error message: ImportError: No module named MolKit Is there any solution for this in Mac? Thank you very much Sing On Feb 18, 2010, at 10:56 AM, pymol-users- requ...@lists.sourceforge.net wrote: Send PyMOL-users mailing list submissions to pymol-users@lists.sourceforge.net To subscribe or unsubscribe via the World Wide Web, visit https://lists.sourceforge.net/lists/listinfo/pymol-users or, via email, send a message with subject or body 'help' to pymol-users-requ...@lists.sourceforge.net You can reach the person managing the list at pymol-users-ow...@lists.sourceforge.net When replying, please edit your Subject line so it is more specific than Re: Contents of PyMOL-users digest... Today's Topics: 1. Autodock plugin (Kin Sing Stephen Lee) 2. Re: Autodock plugin (Daniel Seeliger) 3. Update Submitting Bugs (Jason Vertrees) 4. Re: Update Submitting Bugs (Christoph Gohlke) 5. Re: Update Submitting Bugs (Jason Vertrees) 6. Re: Update Submitting Bugs (Christoph Gohlke) 7. Regarding the Control panel in pymol (phani ghanakota) 8. Re: Regarding the Control panel in pymol (Jason Vertrees) 9. coordinate systems of pymol and povray (Gabriela Schlau-Cohen) -- Message: 1 Date: Tue, 16 Feb 2010 11:06:40 -0800 From: Kin Sing Stephen Lee leek...@msu.edu Subject: [PyMOL] Autodock plugin To: pymol-users@lists.sourceforge.net pymol-users@lists.sourceforge.net Message-ID: 333eebd7-7c78-48d5-90ae-ff9907837...@msu.edu Content-Type: text/plain; charset=US-ASCII; format=flowed; delsp=yes Dear all, This is the first time for me to use the autodock plugin and I have some simple questions. I'm using Macbook Pro (OS X v 10.5 - leopard). Autodock and autodock tools run fine in the X11 terminal. In the autodock plugin, I need to put in the autodock tool program path,so I put in the path where I installed the autodock tool (under applications folder). When I tried to prepare my receptor and ligand file, the plugin cannot find the autodock tools (prepare_receptor4.py as well as prepare_ligand4.py) so I am wondering where I can find the autodock tools program path or is it possible to use the plugin in mac? Thank you very much Sing -- Message: 2 Date: Tue, 16 Feb 2010 20:26:00 +0100 From: Daniel Seeliger dsee...@gwdg.de Subject: Re: [PyMOL] Autodock plugin To: pymol-users@lists.sourceforge.net Message-ID: 201002162026.00620.dsee...@gwdg.de Content-Type: Text/Plain; charset=iso-8859-1 Hi Sing, take a look into ~/.ADplugin/pymol_autodock_plugin.conf and set the path to the autodocktools scripts correctly. Then the plugin should find them. Cheers, Daniel On Tuesday 16 February 2010 08:06:40 pm Kin Sing Stephen Lee wrote: Dear all, This is the first time for me to use the autodock plugin and I have some simple questions. I'm using Macbook Pro (OS X v 10.5 - leopard). Autodock and autodock tools run fine in the X11 terminal. In the autodock plugin, I need to put in the autodock tool program path,so I put in the path where I installed the autodock tool (under applications folder). When I tried to prepare my receptor and ligand file, the plugin cannot find the autodock tools (prepare_receptor4.py as well as prepare_ligand4.py) so I am wondering where I can find the autodock tools program path or is it possible to use the plugin in mac? Thank you very much Sing --- --- SOLARIS 10 is the OS for Data Centers - provides features such as DTrace, Predictive Self Healing and Award Winning ZFS. Get Solaris 10 NOW http://p.sf.net/sfu/solaris-dev2dev ___ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net -- Dr. Daniel Seeliger Computational Biomolecular Dynamics Group Max-Planck-Institute for Biophysical Chemistry Tel. +49 (0) 551-201-2310 http://wwwuser.gwdg.de/~dseelig -- Message: 3 Date: Wed, 17 Feb 2010 14:35:13 -0500 From: Jason Vertrees jason.vertr...@schrodinger.com Subject: [PyMOL] Update Submitting Bugs To: pymol-users@lists.sourceforge.net Message-ID: 79558d781002171135l2f74c6cax60c357bc8e4b...@mail.gmail.com Content-Type: text/plain; charset=ISO-8859-1 PyMOLers, * In order to keep all bugs in one place please email your bugs to h...@schrodinger.com instead of using the SourceForge tracker. Schrodinger has a very nice bug tracker that we use; and, in the end it's just better to not duplicate effort. * I started pushing small changes into the open-source
[PyMOL] Save movie not working
Hi Delano, When I try to save an MPEG from the save movie menu, pymol works on writing out the movie, then i get an error that says mpeg_encode.exe has encounteres a problem and has to close. A file is written with 0 bytes. There was also an error that mpeg_encode was being used by another file/program...I think. Can you help? Thanks, kr -- Kent Rossman, Ph.D. Research Assistant Professor Department of Pharmacology Lineberger Comprehensive Cancer Center UNC-Chapel Hill, CB 7295 Chapel Hill, NC 27599 Tel: 919-962-1057 Fax: 919-966-0162 -- Download Intel#174; Parallel Studio Eval Try the new software tools for yourself. Speed compiling, find bugs proactively, and fine-tune applications for parallel performance. See why Intel Parallel Studio got high marks during beta. http://p.sf.net/sfu/intel-sw-dev ___ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
Re: [PyMOL] PyMOL-users Digest, Vol 45, Issue 10
Dear all,
Sorry I fixed the prepare_ligand4.py problem. However, when I try to
do the autodock in the plugin, the plugin cannot recognize the
receptor so there is no choice available in the receptor in the
docking page. If I click autogrid or autodock, the program shows no
response. Is there any setting I could check and fix it?
Thank you very much
Sing
On Feb 19, 2010, at 9:33 AM, pymol-users-requ...@lists.sourceforge.net
wrote:
Send PyMOL-users mailing list submissions to
pymol-users@lists.sourceforge.net
To subscribe or unsubscribe via the World Wide Web, visit
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or, via email, send a message with subject or body 'help' to
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You can reach the person managing the list at
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When replying, please edit your Subject line so it is more specific
than Re: Contents of PyMOL-users digest...
Today's Topics:
1. Re: coordinate systems of pymol and povray (Tsjerk Wassenaar)
2. FreeMOL (Jason Vertrees)
3. Re: PyMOL-users Digest, Vol 45, Issue 9 (Kin Sing Stephen Lee)
4. Save movie not working (Kent Rossman)
--
Message: 1
Date: Thu, 18 Feb 2010 21:42:39 +0100
From: Tsjerk Wassenaar tsje...@gmail.com
Subject: Re: [PyMOL] coordinate systems of pymol and povray
To: gabriela.schlau-co...@alumni.brown.edu, pymol-users
pymol-users@lists.sourceforge.net
Message-ID:
8ff898151002181242o50721274q14324f2a14209...@mail.gmail.com
Content-Type: text/plain; charset=iso-8859-1
Hi Gabriela,
If you only want to get the molecule back in view and rotate/translate
it to your liking, you can use commands like:
#declare Protein = union { #include protein.inc }
#declare Center = (min_extent(Protein)+max_extent(Protein))/2;
object { Protein translate -Center }
If you want to preserve the view you had in Pymol, you'll need
something more. For this purpose I wrote a set of POV-Ray macros,
which are attached. For this to work, you have to save the view from
get_view(). If you used the (better ;)) second version of make_pov
from the wiki, the view is already saved in the pov-ray file. Place
the macro file somewhere where POV-Ray can find it, and uncomment the
section in the .pov file starting with Uncomment the following
lines :) Now, if you want to add objects to your scene that you have
defined based on the coordinates in the pdb file, you can use
something like:
// This draws a sphere of radius 1 at the origin of your .pdb
coordinate system
sphere { 0, 1 SET_PYMOL_VIEW( PYMOL_VIEW )) }
For more extensive information, read the first section of the file. If
things are still unclear, feel free to contact me. And if you find
that you've managed to do really cool stuff with it, please let me
know :)
Hope it helps,
Tsjerk
On Wed, Feb 17, 2010 at 5:07 PM, Gabriela Schlau-Cohen
gsad...@hotmail.com wrote:
Hi all,
I am trying to load a pymol graphic into povray and then add on
geometric
objects.? I exported and loaded the molecular model from pymol
successfully
using the make_pov.py script from the wiki. ?I can then copy and
paste that
file into povray to generate the molecules through povray. ?Then,
when I
save the object in pymol to get the molecular coordinates, the
coordinates
are in a different system.
Can someone tell me how to get the molecular coordinates and a
povray file
in the same coordinate system?
Thanks,
Gabriela
Hotmail: Trusted email with powerful SPAM protection. Sign up now.
--
Download Intel? Parallel Studio Eval
Try the new software tools for yourself. Speed compiling, find bugs
proactively, and fine-tune applications for parallel performance.
See why Intel Parallel Studio got high marks during beta.
http://p.sf.net/sfu/intel-sw-dev
___
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Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users
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--
Tsjerk A. Wassenaar, Ph.D.
Computational Chemist
Medicinal Chemist
Neuropharmacologist
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Message: 2
Date: Thu, 18 Feb 2010 16:36:40 -0500
From: Jason Vertrees jason.vertr...@schrodinger.com
Subject: [PyMOL] FreeMOL
To: pymol-users@lists.sourceforge.net
Message-ID:
79558d781002181336x4216e157w7181f92f24cbd...@mail.gmail.com
Content-Type: text/plain; charset=ISO-8859-1
PyMOLers,
The FreeMOL website is back up as it was before
Re: [PyMOL] PyMOL-users Digest, Vol 45, Issue 10
Sing,
if there is no receptor listed you probably didn't generate one.
You can do that on the Generate Receptor page.
-Daniel
On Friday 19 February 2010 07:13:58 pm Kin Sing Stephen Lee wrote:
Dear all,
Sorry I fixed the prepare_ligand4.py problem. However, when I try to
do the autodock in the plugin, the plugin cannot recognize the
receptor so there is no choice available in the receptor in the
docking page. If I click autogrid or autodock, the program shows no
response. Is there any setting I could check and fix it?
Thank you very much
Sing
On Feb 19, 2010, at 9:33 AM, pymol-users-requ...@lists.sourceforge.net
wrote:
Send PyMOL-users mailing list submissions to
pymol-users@lists.sourceforge.net
To subscribe or unsubscribe via the World Wide Web, visit
https://lists.sourceforge.net/lists/listinfo/pymol-users
or, via email, send a message with subject or body 'help' to
pymol-users-requ...@lists.sourceforge.net
You can reach the person managing the list at
pymol-users-ow...@lists.sourceforge.net
When replying, please edit your Subject line so it is more specific
than Re: Contents of PyMOL-users digest...
Today's Topics:
1. Re: coordinate systems of pymol and povray (Tsjerk Wassenaar)
2. FreeMOL (Jason Vertrees)
3. Re: PyMOL-users Digest, Vol 45, Issue 9 (Kin Sing Stephen Lee)
4. Save movie not working (Kent Rossman)
--
Message: 1
Date: Thu, 18 Feb 2010 21:42:39 +0100
From: Tsjerk Wassenaar tsje...@gmail.com
Subject: Re: [PyMOL] coordinate systems of pymol and povray
To: gabriela.schlau-co...@alumni.brown.edu, pymol-users
pymol-users@lists.sourceforge.net
Message-ID:
8ff898151002181242o50721274q14324f2a14209...@mail.gmail.com
Content-Type: text/plain; charset=iso-8859-1
Hi Gabriela,
If you only want to get the molecule back in view and rotate/translate
it to your liking, you can use commands like:
#declare Protein = union { #include protein.inc }
#declare Center = (min_extent(Protein)+max_extent(Protein))/2;
object { Protein translate -Center }
If you want to preserve the view you had in Pymol, you'll need
something more. For this purpose I wrote a set of POV-Ray macros,
which are attached. For this to work, you have to save the view from
get_view(). If you used the (better ;)) second version of make_pov
from the wiki, the view is already saved in the pov-ray file. Place
the macro file somewhere where POV-Ray can find it, and uncomment the
section in the .pov file starting with Uncomment the following
lines :) Now, if you want to add objects to your scene that you have
defined based on the coordinates in the pdb file, you can use
something like:
// This draws a sphere of radius 1 at the origin of your .pdb
coordinate system
sphere { 0, 1 SET_PYMOL_VIEW( PYMOL_VIEW )) }
For more extensive information, read the first section of the file. If
things are still unclear, feel free to contact me. And if you find
that you've managed to do really cool stuff with it, please let me
know :)
Hope it helps,
Tsjerk
On Wed, Feb 17, 2010 at 5:07 PM, Gabriela Schlau-Cohen
gsad...@hotmail.com wrote:
Hi all,
I am trying to load a pymol graphic into povray and then add on
geometric
objects.? I exported and loaded the molecular model from pymol
successfully
using the make_pov.py script from the wiki. ?I can then copy and
paste that
file into povray to generate the molecules through povray. ?Then,
when I
save the object in pymol to get the molecular coordinates, the
coordinates
are in a different system.
Can someone tell me how to get the molecular coordinates and a
povray file
in the same coordinate system?
Thanks,
Gabriela
Hotmail: Trusted email with powerful SPAM protection. Sign up now.
-- Download Intel? Parallel Studio Eval
Try the new software tools for yourself. Speed compiling, find bugs
proactively, and fine-tune applications for parallel performance.
See why Intel Parallel Studio got high marks during beta.
http://p.sf.net/sfu/intel-sw-dev
___
PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net)
Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users
Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
--
Tsjerk A. Wassenaar, Ph.D.
Computational Chemist
Medicinal Chemist
Neuropharmacologist
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--
Message: 2
Date: Thu, 18 Feb 2010 16:36:40 -0500
From: Jason
Re: [PyMOL] PyMOL-users Digest, Vol 45, Issue 10
Hello Sing,
Perhaps going over the basic tutorial will help make things clear:
http://wwwuser.gwdg.de/~dseelig/plugin_tutorial.html
Best,
Shiven
On Fri, Feb 19, 2010 at 1:13 PM, Kin Sing Stephen Lee
s...@chemistry.msu.edu wrote:
Dear all,
Sorry I fixed the prepare_ligand4.py problem. However, when I try to
do the autodock in the plugin, the plugin cannot recognize the
receptor so there is no choice available in the receptor in the
docking page. If I click autogrid or autodock, the program shows no
response. Is there any setting I could check and fix it?
Thank you very much
Sing
On Feb 19, 2010, at 9:33 AM, pymol-users-requ...@lists.sourceforge.net
wrote:
Send PyMOL-users mailing list submissions to
pymol-us...@lists.sourceforge.net
To subscribe or unsubscribe via the World Wide Web, visit
https://lists.sourceforge.net/lists/listinfo/pymol-users
or, via email, send a message with subject or body 'help' to
pymol-users-requ...@lists.sourceforge.net
You can reach the person managing the list at
pymol-users-ow...@lists.sourceforge.net
When replying, please edit your Subject line so it is more specific
than Re: Contents of PyMOL-users digest...
Today's Topics:
1. Re: coordinate systems of pymol and povray (Tsjerk Wassenaar)
2. FreeMOL (Jason Vertrees)
3. Re: PyMOL-users Digest, Vol 45, Issue 9 (Kin Sing Stephen Lee)
4. Save movie not working (Kent Rossman)
--
Message: 1
Date: Thu, 18 Feb 2010 21:42:39 +0100
From: Tsjerk Wassenaar tsje...@gmail.com
Subject: Re: [PyMOL] coordinate systems of pymol and povray
To: gabriela.schlau-co...@alumni.brown.edu, pymol-users
pymol-users@lists.sourceforge.net
Message-ID:
8ff898151002181242o50721274q14324f2a14209...@mail.gmail.com
Content-Type: text/plain; charset=iso-8859-1
Hi Gabriela,
If you only want to get the molecule back in view and rotate/translate
it to your liking, you can use commands like:
#declare Protein = union { #include protein.inc }
#declare Center = (min_extent(Protein)+max_extent(Protein))/2;
object { Protein translate -Center }
If you want to preserve the view you had in Pymol, you'll need
something more. For this purpose I wrote a set of POV-Ray macros,
which are attached. For this to work, you have to save the view from
get_view(). If you used the (better ;)) second version of make_pov
from the wiki, the view is already saved in the pov-ray file. Place
the macro file somewhere where POV-Ray can find it, and uncomment the
section in the .pov file starting with Uncomment the following
lines :) Now, if you want to add objects to your scene that you have
defined based on the coordinates in the pdb file, you can use
something like:
// This draws a sphere of radius 1 at the origin of your .pdb
coordinate system
sphere { 0, 1 SET_PYMOL_VIEW( PYMOL_VIEW )) }
For more extensive information, read the first section of the file. If
things are still unclear, feel free to contact me. And if you find
that you've managed to do really cool stuff with it, please let me
know :)
Hope it helps,
Tsjerk
On Wed, Feb 17, 2010 at 5:07 PM, Gabriela Schlau-Cohen
gsad...@hotmail.com wrote:
Hi all,
I am trying to load a pymol graphic into povray and then add on
geometric
objects.? I exported and loaded the molecular model from pymol
successfully
using the make_pov.py script from the wiki. ?I can then copy and
paste that
file into povray to generate the molecules through povray. ?Then,
when I
save the object in pymol to get the molecular coordinates, the
coordinates
are in a different system.
Can someone tell me how to get the molecular coordinates and a
povray file
in the same coordinate system?
Thanks,
Gabriela
Hotmail: Trusted email with powerful SPAM protection. Sign up now.
--
Download Intel? Parallel Studio Eval
Try the new software tools for yourself. Speed compiling, find bugs
proactively, and fine-tune applications for parallel performance.
See why Intel Parallel Studio got high marks during beta.
http://p.sf.net/sfu/intel-sw-dev
___
PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net)
Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users
Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
--
Tsjerk A. Wassenaar, Ph.D.
Computational Chemist
Medicinal Chemist
Neuropharmacologist
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Message: 2
Date: Thu, 18 Feb 2010 16:36:40 -0500
From: Jason Vertrees jason.vertr...@schrodinger.com
Subject: [PyMOL] FreeMOL
To:
