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, [email protected] wrote: > Send PyMOL-users mailing list submissions to > [email protected] > > 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 > [email protected] > > You can reach the person managing the list at > [email protected] > > 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 <[email protected]> > Subject: Re: [PyMOL] coordinate systems of pymol and povray > To: [email protected], pymol-users > <[email protected]> > Message-ID: > <[email protected]> > 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 > <[email protected]> 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 ([email protected]) >> Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users >> Archives: http://www.mail-archive.com/[email protected] >> > > > > -- > 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 <[email protected]> > Subject: [PyMOL] FreeMOL > To: [email protected] > Message-ID: > <[email protected]> > Content-Type: text/plain; charset=ISO-8859-1 > > PyMOLers, > > The FreeMOL website is back up as it was before (http://freemol.org). > FreeMOL is still open-source, based off the original bioinformatics > project. The only difference is the location of the webserver: it is > now running from a Schrodinger server to give me better access (again, > Warren's servers only had FTP access, we now have ssh). > > Please let me know if anything's missing. > > Thanks for being patient, > > -- Jason > > -- > Jason Vertrees, PhD > PyMOL Product Manager > Schrodinger, LLC > > (e) [email protected] > (o) +1 (603) 374-7120 > > > > ------------------------------ > > Message: 3 > Date: Fri, 19 Feb 2010 01:37:24 -0800 > From: Kin Sing Stephen Lee <[email protected]> > Subject: Re: [PyMOL] PyMOL-users Digest, Vol 45, Issue 9 > To: [email protected] > Message-ID: <[email protected]> > Content-Type: text/plain; charset=US-ASCII; format=flowed; delsp=yes > > 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- > [email protected] wrote: > >> Send PyMOL-users mailing list submissions to >> [email protected] >> >> 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 >> [email protected] >> >> You can reach the person managing the list at >> [email protected] >> >> 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 <[email protected]> >> Subject: [PyMOL] Autodock plugin >> To: "[email protected]" >> <[email protected]> >> Message-ID: <[email protected]> >> 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 <[email protected]> >> Subject: Re: [PyMOL] Autodock plugin >> To: [email protected] >> Message-ID: <[email protected]> >> 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 ([email protected]) >>> Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users >>> Archives: http://www.mail-archive.com/[email protected] >>> >> >> -- >> 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 <[email protected]> >> Subject: [PyMOL] Update & Submitting Bugs >> To: [email protected] >> Message-ID: >> <[email protected]> >> Content-Type: text/plain; charset=ISO-8859-1 >> >> PyMOLers, >> >> * In order to keep all bugs in one place please email your bugs to >> [email protected] 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 code and more >> are coming. Please file bugs to the aforementioned address. >> >> * CEAlign is working on all my versions of PyMOL, so I'll be pushing >> that to the open-source soon. >> >> * We now have another server for FreeMOL (which maps right back to >> http://freemol.org/) and we also have control over the FreeMOL >> project. When I get back to my office (where the files live) I'll >> update FreeMOL. >> >> Thanks, >> >> -- Jason >> >> -- >> Jason Vertrees, PhD >> PyMOL Product Manager >> Schrodinger, LLC >> >> (e) [email protected] >> (o) +1 (603) 374-7120 >> >> >> >> ------------------------------ >> >> Message: 4 >> Date: Wed, 17 Feb 2010 21:15:06 -0800 >> From: Christoph Gohlke <[email protected]> >> Subject: Re: [PyMOL] Update & Submitting Bugs >> To: [email protected] >> Message-ID: <[email protected]> >> Content-Type: text/plain; charset=ISO-8859-1 >> >> What is the URL of the Schrodinger bug tracker? The PyMOL SourceForge >> tracker is disabled. >> >> Thanks, >> >> Christoph >> >> >> On 2/17/2010 11:35 AM, Jason Vertrees wrote: >>> PyMOLers, >>> >>> * In order to keep all bugs in one place please email your bugs to >>> [email protected] 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 code and more >>> are coming. Please file bugs to the aforementioned address. >>> >>> * CEAlign is working on all my versions of PyMOL, so I'll be pushing >>> that to the open-source soon. >>> >>> * We now have another server for FreeMOL (which maps right back to >>> http://freemol.org/) and we also have control over the FreeMOL >>> project. When I get back to my office (where the files live) I'll >>> update FreeMOL. >>> >>> Thanks, >>> >>> -- Jason >>> >> >> >> >> ------------------------------ >> >> Message: 5 >> Date: Thu, 18 Feb 2010 00:30:49 -0500 >> From: Jason Vertrees <[email protected]> >> Subject: Re: [PyMOL] Update & Submitting Bugs >> To: Christoph Gohlke <[email protected]> >> Cc: [email protected] >> Message-ID: >> <[email protected]> >> Content-Type: text/plain; charset=ISO-8859-1 >> >> Christoph, >> >> Schrodinger's tracker is internal only. To submit a bug, just email >> your bugs to [email protected] (for faster turnaround put >> something >> like "PyMOL Bug" in the title). They are immediately filed and >> assigned to me. >> >> I chose to turn off the SourceForge tracker because I do not want to >> miss bugs or spend my time duplicating tracking efforts, as I was. >> >> Thanks, >> >> -- Jason >> >> On Thu, Feb 18, 2010 at 12:15 AM, Christoph Gohlke <[email protected]> >> wrote: >>> What is the URL of the Schrodinger bug tracker? The PyMOL >>> SourceForge >>> tracker is disabled. >>> >>> Thanks, >>> >>> Christoph >>> >>> >>> On 2/17/2010 11:35 AM, Jason Vertrees wrote: >>>> PyMOLers, >>>> >>>> * In order to keep all bugs in one place please email your bugs to >>>> [email protected] 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 code and >>>> more >>>> are coming. ?Please file bugs to the aforementioned address. >>>> >>>> * CEAlign is working on all my versions of PyMOL, so I'll be >>>> pushing >>>> that to the open-source soon. >>>> >>>> * We now have another server for FreeMOL (which maps right back to >>>> http://freemol.org/) and we also have control over the FreeMOL >>>> project. ?When I get back to my office (where the files live) I'll >>>> update FreeMOL. >>>> >>>> Thanks, >>>> >>>> -- Jason >>>> >>> >>> ------------------------------------------------------------------------------ >>> 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 ([email protected]) >>> Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users >>> Archives: http://www.mail-archive.com/[email protected] >>> >> >> >> >> -- >> Jason Vertrees, PhD >> PyMOL Product Manager >> Schrodinger, LLC >> >> (e) [email protected] >> (o) +1 (603) 374-7120 >> >> >> >> ------------------------------ >> >> Message: 6 >> Date: Wed, 17 Feb 2010 23:23:26 -0800 >> From: Christoph Gohlke <[email protected]> >> Subject: Re: [PyMOL] Update & Submitting Bugs >> To: Jason Vertrees <[email protected]> >> Cc: [email protected] >> Message-ID: <[email protected]> >> Content-Type: text/plain; charset=ISO-8859-1 >> >> Good. Thanks for keeping PyMOL development going. >> >> Christoph >> >> On 2/17/2010 9:30 PM, Jason Vertrees wrote: >>> Christoph, >>> >>> Schrodinger's tracker is internal only. To submit a bug, just email >>> your bugs to [email protected] (for faster turnaround put >>> something >>> like "PyMOL Bug" in the title). They are immediately filed and >>> assigned to me. >>> >>> I chose to turn off the SourceForge tracker because I do not want to >>> miss bugs or spend my time duplicating tracking efforts, as I was. >>> >>> Thanks, >>> >>> -- Jason >>> >>> On Thu, Feb 18, 2010 at 12:15 AM, Christoph Gohlke >>> <[email protected]> wrote: >>>> What is the URL of the Schrodinger bug tracker? The PyMOL >>>> SourceForge >>>> tracker is disabled. >>>> >>>> Thanks, >>>> >>>> Christoph >>>> >>>> >>>> On 2/17/2010 11:35 AM, Jason Vertrees wrote: >>>>> PyMOLers, >>>>> >>>>> * In order to keep all bugs in one place please email your bugs to >>>>> [email protected] 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 code and >>>>> more >>>>> are coming. Please file bugs to the aforementioned address. >>>>> >>>>> * CEAlign is working on all my versions of PyMOL, so I'll be >>>>> pushing >>>>> that to the open-source soon. >>>>> >>>>> * We now have another server for FreeMOL (which maps right back to >>>>> http://freemol.org/) and we also have control over the FreeMOL >>>>> project. When I get back to my office (where the files live) I'll >>>>> update FreeMOL. >>>>> >>>>> Thanks, >>>>> >>>>> -- Jason >> >> >> >> ------------------------------ >> >> Message: 7 >> Date: Thu, 18 Feb 2010 09:30:34 -0800 (PST) >> From: phani ghanakota <[email protected]> >> Subject: [PyMOL] Regarding the Control panel in pymol >> To: [email protected] >> Message-ID: <[email protected]> >> Content-Type: text/plain; charset="us-ascii" >> >> Hi, >> >> Is there a way to toggle on and off the control panel using a >> command. So that viewing in the full screen mode would be more >> pleasant. >> >> Thanks in advance. >> >> >> >> >> -------------- next part -------------- >> An HTML attachment was scrubbed... >> >> ------------------------------ >> >> Message: 8 >> Date: Thu, 18 Feb 2010 13:54:40 -0500 >> From: Jason Vertrees <[email protected]> >> Subject: Re: [PyMOL] Regarding the Control panel in pymol >> To: phani ghanakota <[email protected]> >> Cc: [email protected] >> Message-ID: >> <[email protected]> >> Content-Type: text/plain; charset=ISO-8859-1 >> >> On Thu, Feb 18, 2010 at 12:30 PM, phani ghanakota >> <[email protected]> wrote: >>> Is there a way to toggle on and off the control panel using a >>> command. So that viewing in the full screen mode would be more >>> pleasant. >> >> Phani, >> >> # turns off the internal UI >> set internal_gui, 0 >> >> # make PyMOL fullscreen; works on Windows and Mac; some issues on >> Linux >> fullscreen >> >> -- Jason >> >> -- >> Jason Vertrees, PhD >> PyMOL Product Manager >> Schrodinger, LLC >> >> (e) [email protected] >> (o) +1 (603) 374-7120 >> >> >> >> ------------------------------ >> >> Message: 9 >> Date: Wed, 17 Feb 2010 16:07:05 +0000 >> From: Gabriela Schlau-Cohen <[email protected]> >> Subject: [PyMOL] coordinate systems of pymol and povray >> To: <[email protected]> >> Message-ID: <[email protected]> >> Content-Type: text/plain; charset="iso-8859-1" >> >> >> 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. >> http://clk.atdmt.com/GBL/go/201469227/direct/01/ >> -------------- next part -------------- >> An HTML attachment was scrubbed... >> >> ------------------------------ >> >> ------------------------------------------------------------------------------ >> 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 >> [email protected] >> https://lists.sourceforge.net/lists/listinfo/pymol-users >> >> >> End of PyMOL-users Digest, Vol 45, Issue 9 >> ****************************************** >> > > > > > ------------------------------ > > Message: 4 > Date: Thu, 18 Feb 2010 22:33:14 -0500 > From: "Kent Rossman" <[email protected]> > Subject: [PyMOL] Save movie not working > To: [email protected] > Message-ID: <[email protected]> > Content-Type: text/plain; charset=iso-8859-1; format=flowed > > 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 > [email protected] > https://lists.sourceforge.net/lists/listinfo/pymol-users > > > End of PyMOL-users Digest, Vol 45, Issue 10 > ******************************************* ------------------------------------------------------------------------------ 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 ([email protected]) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/[email protected]
