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Re: [PyMOL] 2. pymol autodock plugin (Daniel Seeliger)
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From: Daniel S. <ds...@gw...> - 2009-09-18 06:51:00
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Maybe I missed it. What particular problem do you have? Please post the error message you get. Daniel On Thursday 17 September 2009 19:16:13 Kin Sing Stephen Lee wrote: > I have the same problem on loading autodock plugin while i'm using > macpymol 1.1 > > I have installed both numpy and python > > Could you please help me with that? > > Thank you very much > > sing > > > On Sep 17, 2009, at 12:15 PM, pymol-users- > > re...@li... wrote: > > Send PyMOL-users mailing list submissions to > > pym...@li... > > > > 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 > > pym...@li... > > > > You can reach the person managing the list at > > pym...@li... > > > > When replying, please edit your Subject line so it is more specific > > than "Re: Contents of PyMOL-users digest..." > > > > > > Today's Topics: > > > > 1. Re: load dcd files problem (Hugo G. de Teran) > > 2. pymol autodock plugin (Daniel Seeliger) > > 3. movie.roll in middle of movie (Benjamin Bobay) > > 4. Re: movie.roll in middle of movie (Warren DeLano) > > 5. Grid View of a Group (T. Andrew Binkowski) > > > > > > ---------------------------------------------------------------------- > > > > Message: 1 > > Date: Tue, 15 Sep 2009 15:45:56 +0200 > > From: "Hugo G. de Teran" <hug...@us...> > > Subject: Re: [PyMOL] load dcd files problem > > To: Marius Retegan <mar...@gm...> > > Cc: pym...@li... > > Message-ID: <4AA...@us...> > > Content-Type: text/plain; charset=ISO-8859-1 > > > > I did that now, run again > > pymol setup.py build install > > pymol setup2.py install > > but still the same error ... > > > > Hugo > > > > Marius Retegan wrote: > >> Did you uncomment in setup.py the lines related to VMD support? > >> > >> On Tue, Sep 15, 2009 at 3:07 PM, Hugo G. de Teran > >> > >> <hug...@us...> wrote: > >>> Hi, > >>> > >>> I am trying to use the load_traj command to load dcd files. > >>> Holever, I > >>> get the following error: > >>> PyMOL>load_traj ../../1bwb/dc1.dcd, initial, > >>> ObjectMolecule-Error: sorry, VMD Molfile Plugins not compiled into > >>> this > >>> build. > >>> > >>> I have installed pymol from source with the default method (i.e., > >>> python > >>> install scripts) on my opensuse11.1 x86_64 > >>> > >>> Thanks for help, > >>> > >>> Hugo > >>> > >>> > >>> > >>> -- > >>> Hugo G. de Teran, PhD. > >>> "Parga Pondal" Research fellow > >>> Fundaci?n P?blica Galega de Medicina Xen?mica - SERGAS > >>> Santiago de Compostela (SPAIN) > >>> > >>> Phone +34 981563100 ext 13873 > >>> e-mail:hug...@us... <e-mail%3Ah...@us...> > >>> http://web.usc.es/~hugogdt <http://web.usc.es/%7Ehugogdt> > >>> > >>> > >>> > >>> > >>> ----------------------------------------------------------------------- > >>>------- Come build with us! The BlackBerry® Developer Conference in > >>> SF, CA > >>> is the only developer event you need to attend this year. > >>> Jumpstart your > >>> developing skills, take BlackBerry mobile applications to market > >>> and stay > >>> ahead of the curve. Join us from November 9-12, 2009. Register > >>> now! > >>> http://p.sf.net/sfu/devconf > >>> _______________________________________________ > >>> PyMOL-users mailing list (PyM...@li...) > >>> Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users > >>> Archives: http://www.mail-archive.com/pym...@li... > >> > >> --0016e6db2dbbff30f304739dc03a > >> Content-Type: text/html; charset=O-8859-1 > >> Content-Transfer-Encoding: quoted-printable > >> > >> Did you uncomment in setup.py the lines related to VMD support? > >> <br><br><div class="gmail_quote">On Tue, Sep 15, 2009 at 3:07 PM, > >> Hugo G. de Teran <span dir="ltr"><<a href="mailto:hug...@us... > >> ">hDelivered-To: hu...@gm... > >> Received: by 10.103.221.10 with SMTP id y10cs111217muq; > >> Tue, 15 Sep 2009 06:29:04 -0700 (PDT) > >> Received: by 10.211.171.14 with SMTP id y14mr8459245ebo. > >> 58.1253021301179; > >> Tue, 15 Sep 2009 06:28:21 -0700 (PDT) > >> Return-Path: <mar...@gm...> > >> Received: from rojo2.usc.es (rojo2.usc.es [193.144.75.10]) > >> by mx.google.com with ESMTP id 25si5396218ewy. > >> 39.2009.09.15.06.28.19; 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Tue, > >> 15 Sep 2009 06:28:11 -0700 (PDT) > >> In-Reply-To: <4AA...@us...> > >> References: <4AA...@us...> > >> Date: Tue, 15 Sep 2009 15:28:11 +0200 > >> Message-ID: <522...@ma... > >> > >> Subject: Re: [PyMOL] load dcd files problem > >> From: Marius Retegan <mar...@gm...> > >> To: "Hugo G. de Teran" <hug...@us...> > >> Content-Type: multipart/alternative; boundary > >> --0016e6db2dbbff30f304739dc03a > >> Content-Type: text/plain; charset=O-8859-1 > >> Content-Transfer-Encoding: quoted-printable > >> > >> Did you uncomment in setup.py the lines related to VMD support? > >> > >> On Tue, Sep 15, 2009 at 3:07 PM, Hugo G. de Teran > >> > >> <hug...@us...> wrote: > >>> Hi, > >>> > >>> I am trying to use the load_traj command to load dcd files. > >>> Holever, I > >>> get the following error: > >>> PyMOL>load_traj ../../1bwb/dc1.dcd, initial, > >>> ObjectMolecule-Error: sorry, VMD Molfile Plugins not compiled into > >>> this > >>> build. > >>> > >>> I have installed pymol from source with the default method (i.e., > >>> python > >>> install scripts) on my opensuse11.1 x86_64 > >>> > >>> Thanks for help, > >>> > >>> Hugo > >>> > >>> > >>> > >>> -- > >>> Hugo G. de Teran, PhD. > >>> "Parga Pondal" Research fellow > >>> Fundaci?n P?blica Galega de Medicina Xen?mica - SERGAS > >>> Santiago de Compostela (SPAIN) > >>> > >>> Phone +34 981563100 ext 13873 > >>> e-mail:hug...@us... <e-mail%3Ah...@us...> > >>> http://web.usc.es/~hugogdt <http://web.usc.es/%7Ehugogdt> > >>> > >>> > >>> > >>> > >>> ----------------------------------------------------------------------- > >>>------- Come build with us! The BlackBerry® Developer Conference in > >>> SF, CA > >>> is the only developer event you need to attend this year. > >>> Jumpstart your > >>> developing skills, take BlackBerry mobile applications to market > >>> and stay > >>> ahead of the curve. Join us from November 9-12, 2009. Register > >>> now! > >>> http://p.sf.net/sfu/devconf > >>> _______________________________________________ > >>> PyMOL-users mailing list (PyM...@li...) > >>> Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users > >>> Archives: http://www.mail-archive.com/pym...@li... > >> > >> --0016e6db2dbbff30f304739dc03a > >> Content-Type: text/html; charset=O-8859-1 > >> Content-Transfer-Encoding: quoted-printable > >> > >> Did you uncomment in setup.py the lines related to VMD support? > >> <br><br><div class="gmail_quote">On Tue, Sep 15, 2009 at 3:07 PM, > >> Hugo G. de Teran <span dir="ltr"><<a href="mailto:hug...@us... > >> ">hug...@us...</a>></span> wrote:<br> > >> <blockquote class="gmail_quote" style="border-left: 1px solid > >> rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: > >> 1ex;">Hi,<br> > >> <br> > >> I am trying to use the load_traj command to load dcd files. > >> Holever, I<br> > >> get the following error:<br> > >> PyMOL>load_traj ../../1bwb/dc1.dcd, initial,<br> > >> ObjectMolecule-Error: sorry, VMD Molfile Plugins not compiled into > >> this<br> > >> build.<br> > >> <br> > >> I have installed pymol from source with the default method (i.e., > >> python<br> > >> install scripts) on my opensuse11.1 x86_64<br> > >> <br> > >> Thanks for help,<br> > >> <br> > >> Hugo<br> > >> <br> > >> <br> > >> <br> > >> --<br> > >> Hugo G. de Teran, PhD.<br> > >> "Parga Pondal" Research fellow<br> > >> Fundaci?n P?blica Galega de Medicina Xen?mica - SERGAS<br> > >> Santiago de Compostela (SPAIN)<br> > >> <br> > >> Phone +34 981563100 ext 13873<br> > >> <a href="mailto:e-mail%3Ah...@us...">e- > >> mail:hug...@us...</a> <a href="http://web.usc.es/%7Ehugogdt > >> " target="_blank">http://web.usc.es/~hugogdt</a><br> > >> <br> > >> <br> > >> <br> > >> ------------------------------------------------------------------------ > >>------< br> > >> Come build with us! The BlackBerry&reg; Developer Conference in > >> SF, CA<br> > >> is the only developer event you need to attend this year. Jumpstart > >> your<br> > >> developing skills, take BlackBerry mobile applications to market > >> and stay<br> > >> ahead of the curve. Join us from November 9&#45;12, 2009. > >> Register now&#33;<br> > >> <a href="http://p.sf.net/sfu/devconf" > >> target="_blank">http://p.sf.net/sfu/devconf </a><br> > >> _______________________________________________<br> > >> PyMOL-users mailing list (<a > >> href="mailto:PyM...@li... > >> ">PyM...@li...</a>)<br> > >> Info Page: <a > >> href="https://lists.sourceforge.net/lists/listinfo/pymol-users " > >> target="_blank">https://lists.sourceforge.net/lists/listinfo/pymol-users > >> </a><br> > >> Archives: <a > >> href="http://www.mail-archive.com/pym...@li... " > >> target="_blank">http://www.mail-archive.com/pym...@li...urceforg > >>e.net </a><br> > >> </blockquote></div><br> > >> > >> --0016e6db2dbbff30f304739dc03a-- > > > > -- > > Hugo G. de Teran, PhD. > > "Parga Pondal" Research fellow > > Fundaci?n P?blica Galega de Medicina Xen?mica - SERGAS > > Santiago de Compostela (SPAIN) > > > > Phone +34 981563100 ext 13873 > > e-mail:hug...@us... http://web.usc.es/~hugogdt > > > > > > > > > > > > ------------------------------ > > > > Message: 2 > > Date: Wed, 16 Sep 2009 22:09:02 +0200 > > From: Daniel Seeliger <ds...@gw...> > > Subject: [PyMOL] pymol autodock plugin > > To: pym...@li... > > Message-ID: <200...@gw...> > > Content-Type: text/plain; charset="iso-8859-1" > > > > Dear PyMOLers, > > > > there is a new version of the plugin on the web > > (http://wwwuser.gwdg.de/~dseelig/adplugin.html). > > > > It contains a bunch of new features, like: > > - setup and execution of complete docking runs > > - support for VINA (http://vina.scripps.edu), a great new Autodock > > spawn > > - viewing of Autodock grid maps in PyMOL > > - some lightweight virtual screening functionality > > > > So far it's only tested on Linux and by myself so I expect it to be > > somewhat > > buggy and unstable. Therefore please report bugs. > > > > Cheers, > > Daniel > > > > On Thursday 13 August 2009 22:36:14 Warren DeLano wrote: > >> Jed, > >> > >> With the 1.2 release of PyMOL, we have completely switched over to > >> Numpy. So the first thing to try is to replace: > >> > >> from Numeric import * > >> > >> # with > >> > >> from numpy import * > >> > >> Cheers, > >> Warren > >> > >>> -----Original Message----- > >>> From: Jed Goldstone [mailto:jedgold@MIT.EDU] > >>> Sent: Thursday, August 13, 2009 1:34 PM > >>> To: pym...@li... > >>> Subject: [PyMOL] pymol autodock plugin > >>> > >>> The autodock plugin written by Daniel Seeliger ceased to function > >> > >> (load) > >> > >>> when I upgraded to Pymol 1.2r1. > >>> Although it is not compatible directly with Autodock 4, it did have > >> > >> the > >> > >>> useful functionality of > >>> presenting an autodock 'box' that was readily tweakable, so that the > >>> parameters could be exported for > >>> Autodock Vina. I would LOVE to have this resurrected, but I don't > >>> know > >>> python - can anybody help with this? > >>> > >>> The specific failures I got were: > >>> > >>> File "C:\Program Files\PyMOL/modules\pmg_tk\startup\autodock.py", > >>> line > >> > >> 16, > >> > >>> in <module> > >>> from Numeric import * > >>> ImportError: No module named Numeric > >>> Error: unable to initialize plugin 'autodock'. > >>> > >>> > >>> Any help would be greatly appreciated. > >>> > >>> Jed > >> > >> ------------------------------------------------------------------------ > >> -- > >> > >>> ---- > >>> Jed Goldstone > >>> Research Specialist > >>> Woods Hole Oceanographic Institution > >>> Redfield 3-52 MS #32 > >>> Woods Hole, MA 02543 > >>> http://www.mit.edu/people/jedgold/home.html > >>> (508) 685-2253 (cell/home) (508) 289-4823 (work/WHOI) > >> > >> ------------------------------------------------------------------------ > >> -- > >> > >>> ---- > >>> Let Crystal Reports handle the reporting - Free Crystal Reports 2008 > >> > >> 30- > >> > >>> Day > >>> trial. Simplify your report design, integration and deployment - and > >> > >> focus > >> > >>> on > >>> what you do best, core application coding. Discover what's new with > >>> Crystal Reports now. http://p.sf.net/sfu/bobj-july > >>> _______________________________________________ > >>> PyMOL-users mailing list (PyM...@li...) > >>> Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users > >>> Archives: > >> > >> http://www.mail-archive.com/pym...@li... > >> > >> > >> > >> > >> > >> > >> ------------------------------------------------------------------------ > >>--- --- Let Crystal Reports handle the reporting - Free Crystal Reports > >> 2008 > >> 30-Day trial. Simplify your report design, integration and > >> deployment - and > >> focus on what you do best, core application coding. Discover what's > >> new > >> with Crystal Reports now. http://p.sf.net/sfu/bobj-july > >> _______________________________________________ > >> PyMOL-users mailing list (PyM...@li...) > >> Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users > >> Archives: http://www.mail-archive.com/pym...@li... > > > > -- > > Dr. Daniel Seeliger > > Computational Biomolecular Dynamics Group > > Max-Planck-Institute for Biophysical Chemistry > > Am Fassberg 11 > > 37077 Goettingen, Germany > > Tel: +49 551 201 2310 > > Fax: +49 551 201 2302 > > email: ds...@gw... > > web: http://wwwuser.gwdg.de/~dseelig > > > > > > > > ------------------------------ > > > > Message: 3 > > Date: Wed, 16 Sep 2009 12:47:51 -0400 > > From: Benjamin Bobay <ben...@gm...> > > Subject: [PyMOL] movie.roll in middle of movie > > To: pym...@li... > > Message-ID: <332...@gm...> > > Content-Type: text/plain; charset=US-ASCII; format=flowed; delsp=yes > > > > Good afternoon all - > > > > I think I have a simple question. I would like to have a series of > > "zooms" followed by a movie.roll and then zooming back to the start > > position. Here is what I have > > > > cmd.mset("1 x800") > > cmd.zoom("center","200") > > cmd.frame("1") > > cmd.mview("store") > > cmd.zoom("center","50") > > cmd.frame("120") > > cmd.mview("store") > > cmd.frame("180") > > cmd.mview("store") > > cmd.zoom("center","15") > > cmd.frame("280") > > cmd.mview("store") > > cmd.frame("360") > > cmd.mview("store") > > cmd.zoom("center","50") > > cmd.frame("400") > > cmd.mview("store") > > cmd.frame("420") > > cmd.mview("store") > > cmd.movie.roll("421","755") > > cmd.mview("store") > > cmd.frame("756") > > cmd.mview("store") > > cmd.zoom("center","200") > > cmd.frame("800") > > cmd.mview("reinterpolate") > > > > The problem is that is does not do the movie.roll and as the movie > > plays over and over it actually performs all the zoom actions and then > > rotates one frame and then starts the process again from that newly > > rotated frame. > > > > I would like it to perform the full rotation after the initial zoom > > and then perform the final zoom command. > > > > Any ideas where I might have messed this up? > > > > Many thanks > > Ben > > > > > > > > ------------------------------ > > > > Message: 4 > > Date: Wed, 16 Sep 2009 21:05:36 -0700 > > From: "Warren DeLano" <wa...@de...> > > Subject: Re: [PyMOL] movie.roll in middle of movie > > To: "Benjamin Bobay" <ben...@gm...>, > > <pym...@li...> > > Message-ID: > > <896...@pl...lsci.local> > > Content-Type: text/plain; charset="us-ascii" > > > > Note that this kind of stuff is much easier in PyMOL 1.2 without any > > scripting. > > > > (ScreenCasts for PyMOL Sponsors at http://delsci.info/id/media:new12 > > under "Complex Movie Creation" -- login first). > > > > Nevertheless, a possible answer is below: > > > > Cheers, > > Warren > > > > # PyMOL .pml file (tested against PyMOL 1.2) > > > > load $PYMOL_PATH/test/dat/1tii.pdb > > > > unset movie_auto_interpolate > > unset movie_loop > > > > mset 1 x800 > > > > zoom center,200 > > frame 1 > > mview store > > > > zoom center,50 > > frame 120 > > mview store > > frame 180 > > mview store > > > > zoom center,15 > > frame 280 > > mview store > > frame 360 > > mview store > > > > zoom center,50 > > frame 400 > > mview store > > frame 420 > > mview store > > > > mview interpolate > > > > # instead of: movie.roll 421,755 > > > > frame 531 > > turn y,120 > > mview store > > > > frame 642 > > turn y,120 > > mview store > > > > frame 756 > > turn y,120 > > mview store > > mview interpolate, power=1 > > > > zoom center,200 > > frame 800 > > > > set movie_loop > > mview interpolate > > > > mview smooth > > > > mplay > > > >> -----Original Message----- > >> From: Benjamin Bobay [mailto:ben...@gm...] > >> Sent: Wednesday, September 16, 2009 8:41 PM > >> To: pym...@li... > >> Subject: [PyMOL] movie.roll in middle of movie > >> > >> Good afternoon all - > >> > >> I think I have a simple question. I would like to have a series of > >> "zooms" followed by a movie.roll and then zooming back to the start > >> position. Here is what I have > >> > >> cmd.mset("1 x800") > >> cmd.zoom("center","200") > >> cmd.frame("1") > >> cmd.mview("store") > >> cmd.zoom("center","50") > >> cmd.frame("120") > >> cmd.mview("store") > >> cmd.frame("180") > >> cmd.mview("store") > >> cmd.zoom("center","15") > >> cmd.frame("280") > >> cmd.mview("store") > >> cmd.frame("360") > >> cmd.mview("store") > >> cmd.zoom("center","50") > >> cmd.frame("400") > >> cmd.mview("store") > >> cmd.frame("420") > >> cmd.mview("store") > >> cmd.movie.roll("421","755") > >> cmd.mview("store") > >> cmd.frame("756") > >> cmd.mview("store") > >> cmd.zoom("center","200") > >> cmd.frame("800") > >> cmd.mview("reinterpolate") > >> > >> The problem is that is does not do the movie.roll and as the movie > >> plays over and over it actually performs all the zoom actions and > >> then > >> rotates one frame and then starts the process again from that newly > >> rotated frame. > >> > >> I would like it to perform the full rotation after the initial zoom > >> and then perform the final zoom command. > >> > >> Any ideas where I might have messed this up? > >> > >> Many thanks > >> Ben > > > > ------------------------------------------------------------------------ > > -- > > > >> ---- > >> Come build with us! The BlackBerry® Developer Conference in SF, > >> CA > >> is the only developer event you need to attend this year. Jumpstart > > > > your > > > >> developing skills, take BlackBerry mobile applications to market and > > > > stay > > > >> ahead of the curve. Join us from November 9-12, 2009. Register > >> now! > >> http://p.sf.net/sfu/devconf > >> _______________________________________________ > >> PyMOL-users mailing list (PyM...@li...) > >> Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users > >> Archives: > > > > http://www.mail-archive.com/pym...@li... > > > > > > > > > > > > > > > > > > ------------------------------ > > > > Message: 5 > > Date: Thu, 17 Sep 2009 11:03:03 -0500 > > From: "T. Andrew Binkowski" <abi...@an...> > > Subject: [PyMOL] Grid View of a Group > > To: pym...@li... > > Message-ID: <0B8...@an...> > > Content-Type: text/plain; charset=US-ASCII; format=flowed; delsp=yes > > > > Hi, > > I noticed that in the Grid view that a group of objects is in each > > view. > > > > For example: > > Group A has protein1, protein2 and protein 3. > > Group B has protein 4 and protein 5. > > > > In the grid view there are two views:Group A and GroupB. Is it > > possible to have the grid view have 5 views, one of each molecule? > > > > Thanks, > > Andrew > > > > > > > > > > ------------------------------ > > > > ------------------------------------------------------------------------- > >----- Come build with us! The BlackBerry® Developer Conference in SF, > > CA is the only developer event you need to attend this year. Jumpstart > > your > > developing skills, take BlackBerry mobile applications to market and > > stay > > ahead of the curve. Join us from November 9-12, 2009. Register > > now! > > http://p.sf.net/sfu/devconf > > > > ------------------------------ > > > > _______________________________________________ > > PyMOL-users mailing list > > PyM...@li... > > https://lists.sourceforge.net/lists/listinfo/pymol-users > > > > > > End of PyMOL-users Digest, Vol 40, Issue 12 > > ******************************************* > > --------------------------------------------------------------------------- >--- Come build with us! The BlackBerry® Developer Conference in SF, CA > is the only developer event you need to attend this year. Jumpstart your > developing skills, take BlackBerry mobile applications to market and stay > ahead of the curve. Join us from November 9-12, 2009. Register now! > http://p.sf.net/sfu/devconf > _______________________________________________ > PyMOL-users mailing list (PyM...@li...) > Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users > Archives: http://www.mail-archive.com/pym...@li... -- Dr. Daniel Seeliger Computational Biomolecular Dynamics Group Max-Planck-Institute for Biophysical Chemistry Am Fassberg 11 37077 Goettingen, Germany Tel: +49 551 201 2310 Fax: +49 551 201 2302 email: ds...@gw... web: http://wwwuser.gwdg.de/~dseelig |