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
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
>> Subject: Re: [PyMOL] coordinate systems of pymol and povray
>> To: gabriela.schlau-co...@alumni.brown.edu, pymol-users
>>
>> 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
>> 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
>> -- next part --
>> A non-text attachment was scrubbed...
>> Name: pymolmacro.inc.gz
>> Type: application/x-gzip
>> Size: 2390 bytes
>> Desc: not
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
> > Subject: Re: [PyMOL] coordinate systems of pymol and povray
> > To: gabriela.schlau-co...@alumni.brown.edu, pymol-users
> >
> > 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
> >
> > 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
> > -- next part --
> > A non-text attachment was scru
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
> Subject: Re: [PyMOL] coordinate systems of pymol and povray
> To: gabriela.schlau-co...@alumni.brown.edu, pymol-users
>
> 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
> 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
> -- next part --
> A non-text attachment was scrubbed...
> Name: pymolmacro.inc.gz
> Type: application/x-gzip
> Size: 2390 bytes
> Desc: not available
>
> --
>
> Message: 2
> Date: Thu, 18 Feb 2010 16:36:40 -0500
> From: Jason Vertrees
> Subject: [PyMOL] FreeMOL
> To: pymol-users@lists.sourceforge.net
> Message-ID:
><79558d781002181336x4216e157w7181f92f24cbd...@mail.gmail.com>
> Content-Type: text/plain; charset=ISO-8859-1
>
> PyMOL
[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® 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 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 > Subject: [PyMOL] Autodock plugin > To: "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 > 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 > 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 jus
