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 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) jason.vertr...@schrodinger.com > (o) +1 (603) 374-7120 > > > > ------------------------------ > > Message: 4 > Date: Wed, 17 Feb 2010 21:15:06 -0800 > From: Christoph Gohlke <cgoh...@uci.edu> > Subject: Re: [PyMOL] Update & Submitting Bugs > To: pymol-users@lists.sourceforge.net > Message-ID: <4b7cccda.90...@uci.edu> > 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 >> 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 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 <jason.vertr...@schrodinger.com> > Subject: Re: [PyMOL] Update & Submitting Bugs > To: Christoph Gohlke <cgoh...@uci.edu> > Cc: pymol-users@lists.sourceforge.net > Message-ID: > <79558d781002172130y46763880j59563bd7a908c...@mail.gmail.com> > Content-Type: text/plain; charset=ISO-8859-1 > > Christoph, > > Schrodinger's tracker is internal only. To submit a bug, just email > your bugs to h...@schrodinger.com (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 <cgoh...@uci.edu> > 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 >>> 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 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 (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 >> > > > > -- > Jason Vertrees, PhD > PyMOL Product Manager > Schrodinger, LLC > > (e) jason.vertr...@schrodinger.com > (o) +1 (603) 374-7120 > > > > ------------------------------ > > Message: 6 > Date: Wed, 17 Feb 2010 23:23:26 -0800 > From: Christoph Gohlke <cgoh...@uci.edu> > Subject: Re: [PyMOL] Update & Submitting Bugs > To: Jason Vertrees <jason.vertr...@schrodinger.com> > Cc: pymol-users@lists.sourceforge.net > Message-ID: <4b7ceaee.4000...@uci.edu> > 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 h...@schrodinger.com (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 >> <cgoh...@uci.edu> 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 >>>> 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 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 <gphanionl...@yahoo.com> > Subject: [PyMOL] Regarding the Control panel in pymol > To: pymol-users@lists.sourceforge.net > Message-ID: <820965.90400...@web110014.mail.gq1.yahoo.com> > 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 <jason.vertr...@schrodinger.com> > Subject: Re: [PyMOL] Regarding the Control panel in pymol > To: phani ghanakota <gphanionl...@yahoo.com> > Cc: pymol-users@lists.sourceforge.net > Message-ID: > <79558d781002181054o70d34b6h803e7d385c88e...@mail.gmail.com> > Content-Type: text/plain; charset=ISO-8859-1 > > On Thu, Feb 18, 2010 at 12:30 PM, phani ghanakota > <gphanionl...@yahoo.com> 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) jason.vertr...@schrodinger.com > (o) +1 (603) 374-7120 > > > > ------------------------------ > > Message: 9 > Date: Wed, 17 Feb 2010 16:07:05 +0000 > From: Gabriela Schlau-Cohen <gsad...@hotmail.com> > Subject: [PyMOL] coordinate systems of pymol and povray > To: <pymol-users@lists.sourceforge.net> > Message-ID: <snt109-w258456a7a08f0be0bf5c52a4...@phx.gbl> > 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 > PyMOL-users@lists.sourceforge.net > https://lists.sourceforge.net/lists/listinfo/pymol-users > > > End of PyMOL-users Digest, Vol 45, Issue 9 > ****************************************** > ------------------------------------------------------------------------------ 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
