Re: [PyMOL] PyMOL-users Digest, Vol 45, Issue 10
Hello,
I have gone through the tutorial and follow every single step. The
plugin said it successfully generate the receptor pdbqt file.
However, when I get to the docking, it still cannot detect the
receptor so I cannot run any autogrid or autodock. Is there any reason
for that?
Thank you very much!
Sing
On Feb 19, 2010, at 11:41 AM, Shiven Shandilya wrote:
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:
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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.
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Medicinal
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
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
___
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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:
