[PyMOL] get coordinates
Hi all, Is there an easy way to get coordinates of a given atom? e.g. 'get_coordinates /model//A/ALA`76/CA' for the CA coordinates of resi 76 All the examples on the wiki use iterate to get the coordinates of a selection. Is there a simple way to get one coordinate of a given atom? -- Bradley J. Hintze Graduate Student Duke University School of Medicine 801-712-8799 -- This SF.net email is sponsored by Sprint What will you do first with EVO, the first 4G phone? Visit sprint.com/first -- http://p.sf.net/sfu/sprint-com-first ___ 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] get coordinates
Hi Bradley, print cmd.get_atom_coords(76/CA) Cheers, -- Jason On Tue, Jul 20, 2010 at 5:39 PM, Bradley Hintze bradle...@aggiemail.usu.edu wrote: Hi all, Is there an easy way to get coordinates of a given atom? e.g. 'get_coordinates /model//A/ALA`76/CA' for the CA coordinates of resi 76 All the examples on the wiki use iterate to get the coordinates of a selection. Is there a simple way to get one coordinate of a given atom? -- Bradley J. Hintze Graduate Student Duke University School of Medicine 801-712-8799 -- This SF.net email is sponsored by Sprint What will you do first with EVO, the first 4G phone? Visit sprint.com/first -- http://p.sf.net/sfu/sprint-com-first ___ 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 -- This SF.net email is sponsored by Sprint What will you do first with EVO, the first 4G phone? Visit sprint.com/first -- http://p.sf.net/sfu/sprint-com-first ___ 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
[PyMOL] Fwd: Help setting apbs tools2 on Mac
I want to bring to your attention the wiki entry I posted in pymolwiki regarding the default loading paths for apbs: After installing with fink, none of the default paths work. http://pymolwiki.org/index.php/Talk:APBS#Making_the_default_paths_to_work.3F If someone knows what is going on, please drop a line! Many thanks in advance, Daniel Ra -- Forwarded message -- From: RaDaniel Christian 성준 renderea...@gmail.com Date: Mon, Jun 7, 2010 at 7:07 PM Subject: Help setting apbs tools2 on Mac To: supp...@delsci.com Can I get help with setting configuration files on pymol (cvs fink version1.2r3pre)? I modified the apbsplugin.py to have the following default locations (taken from http://www.poissonboltzmann.org/apbs/examples/visualization/apbs-electrostatics-in-pymol#TOC-Visualization-through-the-new-APBS- OR http://pymolapbsplugin.svn.sourceforge.net/viewvc/pymolapbsplugin/trunk/src/apbsplugin.py) : APBS_BINARY_LOCATION = '/sw64/bin/apbs-mpi-openmpi' APBS_PSIZE_LOCATION = '/sw64/share/apbs-mpi-openmpi/tools/manip/psize.py' APBS_PDB2PQR_LOCATION = '/sw64/bin/pdb2pqr' TEMPORARY_FILE_DIR = '/apbstemp' but after installing by running xpymol as root, I still get this error: Search dirs ['/sw64/lib/pymol-py26/ext/bin', '/sw64/lib/pymol-py26/freemol/bin', '/sw64/lib/pymol-py26/freemol/share/apbs', '/sw64/lib/pymol-py26/freemol/share/pdb2pqr', '/sw64/bin/apbs-mpi-openmpi', '/sw64/share/apbs-mpi-openmpi/tools/manip/psize.py', '/sw64/bin/pdb2pqr', '/sw/share/pdb2pqr', '/usr/local/phenix-dev-403/build/mac-intel-osx/bin', '/sw64/bin', '/sw64/sbin', '/usr/bin', '/bin', '/usr/sbin', '/sbin', '/usr/local/bin', '/usr/X11/bin', '/usr/libexec', '/Developer/Tools', '/usr/X11R6/bin', '/sw64/share/xtal/ccp4-6.1.3/etc', '/sw64/share/xtal/ccp4-6.1.3/bin', '/sw64/share/xtal/ccp4-6.1.3/ccp4i/bin', '/sw64/share/xtal/ccp4-6.1.3/share/dbccp4i/bin', '/sw64/share/xtal/ccp4-6.1.3/share/XIAROOT/xia2/Applications', '/usr/local/xia2-0.3.1.6/xia2core-0.3.1.6/Test', '/usr/local/xia2-0.3.1.6/xia2core-0.3.1.6/Test/Compiled/mac_386', '/usr/local/xia2-0.3.1.6/xia2-0.3.1.6/Applications', '/usr/local/bin', '/opt/local/bin', '/sw/bin'] get_default_location will search the following: ['/sw64/lib/pymol-py26/ext/bin', '/sw64/lib/pymol-py26/freemol/bin', '/sw64/lib/pymol-py26/freemol/share/apbs', '/sw64/lib/pymol-py26/freemol/share/pdb2pqr', '/sw64/bin/apbs-mpi-openmpi', '/sw64/share/apbs-mpi-openmpi/tools/manip/psize.py', '/sw64/bin/pdb2pqr', '/sw/share/pdb2pqr', '/usr/local/phenix-dev-403/build/mac-intel-osx/bin', '/sw64/bin', '/sw64/sbin', '/usr/bin', '/bin', '/usr/sbin', '/sbin', '/usr/local/bin', '/usr/X11/bin', '/usr/libexec', '/Developer/Tools', '/usr/X11R6/bin', '/sw64/share/xtal/ccp4-6.1.3/etc', '/sw64/share/xtal/ccp4-6.1.3/bin', '/sw64/share/xtal/ccp4-6.1.3/ccp4i/bin', '/sw64/share/xtal/ccp4-6.1.3/share/dbccp4i/bin', '/sw64/share/xtal/ccp4-6.1.3/share/XIAROOT/xia2/Applications', '/usr/local/xia2-0.3.1.6/xia2core-0.3.1.6/Test', '/usr/local/xia2-0.3.1.6/xia2core-0.3.1.6/Test/Compiled/mac_386', '/usr/local/xia2-0.3.1.6/xia2-0.3.1.6/Applications', '/usr/local/bin', '/opt/local/bin', '/sw/bin'] trying /sw64/lib/pymol-py26/ext/bin/psize.py trying /sw64/lib/pymol-py26/ext/bin/psize trying /sw64/lib/pymol-py26/freemol/bin/psize.py trying /sw64/lib/pymol-py26/freemol/bin/psize trying /sw64/lib/pymol-py26/freemol/share/apbs/psize.py trying /sw64/lib/pymol-py26/freemol/share/apbs/psize trying /sw64/lib/pymol-py26/freemol/share/pdb2pqr/psize.py trying /sw64/lib/pymol-py26/freemol/share/pdb2pqr/psize trying /sw64/bin/apbs-mpi-openmpi/psize.py trying /sw64/bin/apbs-mpi-openmpi/psize trying /sw64/share/apbs-mpi-openmpi/tools/manip/psize.py/psize.py trying /sw64/share/apbs-mpi-openmpi/tools/manip/psize.py/psize trying /sw64/bin/pdb2pqr/psize.py trying /sw64/bin/pdb2pqr/psize trying /sw/share/pdb2pqr/psize.py trying /sw/share/pdb2pqr/psize trying /usr/local/phenix-dev-403/build/mac-intel-osx/bin/psize.py trying /usr/local/phenix-dev-403/build/mac-intel-osx/bin/psize trying /sw64/bin/psize.py trying /sw64/bin/psize trying /sw64/sbin/psize.py trying /sw64/sbin/psize trying /usr/bin/psize.py trying /usr/bin/psize trying /bin/psize.py trying /bin/psize trying /usr/sbin/psize.py trying /usr/sbin/psize trying /sbin/psize.py trying /sbin/psize trying /usr/local/bin/psize.py trying /usr/local/bin/psize trying /usr/X11/bin/psize.py trying /usr/X11/bin/psize trying /usr/libexec/psize.py trying /usr/libexec/psize trying /Developer/Tools/psize.py trying /Developer/Tools/psize trying /usr/X11R6/bin/psize.py trying /usr/X11R6/bin/psize trying /sw64/share/xtal/ccp4-6.1.3/etc/psize.py trying /sw64/share/xtal/ccp4-6.1.3/etc/psize trying /sw64/share/xtal/ccp4-6.1.3/bin/psize.py trying /sw64/share/xtal/ccp4-6.1.3/bin/psize trying /sw64/share/xtal/ccp4-6.1.3/ccp4i/bin/psize.py trying /sw64/share/xtal/ccp4-6.1.3/ccp4i/bin/psize trying /sw64/share/xtal/ccp4-6.1.3/share/dbccp4i/bin/psize.py trying /sw64/share/xtal/ccp4-6.1.3/share/dbccp4i/bin/psize trying
[PyMOL] Pymol and APBS
Edited the subject. Thanks! On Tue, Jul 20, 2010 at 6:15 PM, RaDaniel Christian 성준 renderea...@gmail.com wrote: I want to bring to your attention the wiki entry I posted in pymolwiki regarding the default loading paths for apbs: After installing with fink, none of the default paths work. http://pymolwiki.org/index.php/Talk:APBS#Making_the_default_paths_to_work.3F If someone knows what is going on, please drop a line! Many thanks in advance, Daniel Ra -- Forwarded message -- From: RaDaniel Christian 성준 renderea...@gmail.com Date: Mon, Jun 7, 2010 at 7:07 PM Subject: Help setting apbs tools2 on Mac To: supp...@delsci.com Can I get help with setting configuration files on pymol (cvs fink version1.2r3pre)? I modified the apbsplugin.py to have the following default locations (taken from http://www.poissonboltzmann.org/apbs/examples/visualization/apbs-electrostatics-in-pymol#TOC-Visualization-through-the-new-APBS- OR http://pymolapbsplugin.svn.sourceforge.net/viewvc/pymolapbsplugin/trunk/src/apbsplugin.py) : APBS_BINARY_LOCATION = '/sw64/bin/apbs-mpi-openmpi' APBS_PSIZE_LOCATION = '/sw64/share/apbs-mpi-openmpi/tools/manip/psize.py' APBS_PDB2PQR_LOCATION = '/sw64/bin/pdb2pqr' TEMPORARY_FILE_DIR = '/apbstemp' but after installing by running xpymol as root, I still get this error: Search dirs ['/sw64/lib/pymol-py26/ext/bin', '/sw64/lib/pymol-py26/freemol/bin', '/sw64/lib/pymol-py26/freemol/share/apbs', '/sw64/lib/pymol-py26/freemol/share/pdb2pqr', '/sw64/bin/apbs-mpi-openmpi', '/sw64/share/apbs-mpi-openmpi/tools/manip/psize.py', '/sw64/bin/pdb2pqr', '/sw/share/pdb2pqr', '/usr/local/phenix-dev-403/build/mac-intel-osx/bin', '/sw64/bin', '/sw64/sbin', '/usr/bin', '/bin', '/usr/sbin', '/sbin', '/usr/local/bin', '/usr/X11/bin', '/usr/libexec', '/Developer/Tools', '/usr/X11R6/bin', '/sw64/share/xtal/ccp4-6.1.3/etc', '/sw64/share/xtal/ccp4-6.1.3/bin', '/sw64/share/xtal/ccp4-6.1.3/ccp4i/bin', '/sw64/share/xtal/ccp4-6.1.3/share/dbccp4i/bin', '/sw64/share/xtal/ccp4-6.1.3/share/XIAROOT/xia2/Applications', '/usr/local/xia2-0.3.1.6/xia2core-0.3.1.6/Test', '/usr/local/xia2-0.3.1.6/xia2core-0.3.1.6/Test/Compiled/mac_386', '/usr/local/xia2-0.3.1.6/xia2-0.3.1.6/Applications', '/usr/local/bin', '/opt/local/bin', '/sw/bin'] get_default_location will search the following: ['/sw64/lib/pymol-py26/ext/bin', '/sw64/lib/pymol-py26/freemol/bin', '/sw64/lib/pymol-py26/freemol/share/apbs', '/sw64/lib/pymol-py26/freemol/share/pdb2pqr', '/sw64/bin/apbs-mpi-openmpi', '/sw64/share/apbs-mpi-openmpi/tools/manip/psize.py', '/sw64/bin/pdb2pqr', '/sw/share/pdb2pqr', '/usr/local/phenix-dev-403/build/mac-intel-osx/bin', '/sw64/bin', '/sw64/sbin', '/usr/bin', '/bin', '/usr/sbin', '/sbin', '/usr/local/bin', '/usr/X11/bin', '/usr/libexec', '/Developer/Tools', '/usr/X11R6/bin', '/sw64/share/xtal/ccp4-6.1.3/etc', '/sw64/share/xtal/ccp4-6.1.3/bin', '/sw64/share/xtal/ccp4-6.1.3/ccp4i/bin', '/sw64/share/xtal/ccp4-6.1.3/share/dbccp4i/bin', '/sw64/share/xtal/ccp4-6.1.3/share/XIAROOT/xia2/Applications', '/usr/local/xia2-0.3.1.6/xia2core-0.3.1.6/Test', '/usr/local/xia2-0.3.1.6/xia2core-0.3.1.6/Test/Compiled/mac_386', '/usr/local/xia2-0.3.1.6/xia2-0.3.1.6/Applications', '/usr/local/bin', '/opt/local/bin', '/sw/bin'] trying /sw64/lib/pymol-py26/ext/bin/psize.py trying /sw64/lib/pymol-py26/ext/bin/psize trying /sw64/lib/pymol-py26/freemol/bin/psize.py trying /sw64/lib/pymol-py26/freemol/bin/psize trying /sw64/lib/pymol-py26/freemol/share/apbs/psize.py trying /sw64/lib/pymol-py26/freemol/share/apbs/psize trying /sw64/lib/pymol-py26/freemol/share/pdb2pqr/psize.py trying /sw64/lib/pymol-py26/freemol/share/pdb2pqr/psize trying /sw64/bin/apbs-mpi-openmpi/psize.py trying /sw64/bin/apbs-mpi-openmpi/psize trying /sw64/share/apbs-mpi-openmpi/tools/manip/psize.py/psize.py trying /sw64/share/apbs-mpi-openmpi/tools/manip/psize.py/psize trying /sw64/bin/pdb2pqr/psize.py trying /sw64/bin/pdb2pqr/psize trying /sw/share/pdb2pqr/psize.py trying /sw/share/pdb2pqr/psize trying /usr/local/phenix-dev-403/build/mac-intel-osx/bin/psize.py trying /usr/local/phenix-dev-403/build/mac-intel-osx/bin/psize trying /sw64/bin/psize.py trying /sw64/bin/psize trying /sw64/sbin/psize.py trying /sw64/sbin/psize trying /usr/bin/psize.py trying /usr/bin/psize trying /bin/psize.py trying /bin/psize trying /usr/sbin/psize.py trying /usr/sbin/psize trying /sbin/psize.py trying /sbin/psize trying /usr/local/bin/psize.py trying /usr/local/bin/psize trying /usr/X11/bin/psize.py trying /usr/X11/bin/psize trying /usr/libexec/psize.py trying /usr/libexec/psize trying /Developer/Tools/psize.py trying /Developer/Tools/psize trying /usr/X11R6/bin/psize.py trying /usr/X11R6/bin/psize trying /sw64/share/xtal/ccp4-6.1.3/etc/psize.py trying /sw64/share/xtal/ccp4-6.1.3/etc/psize trying /sw64/share/xtal/ccp4-6.1.3/bin/psize.py trying /sw64/share/xtal/ccp4-6.1.3/bin/psize trying
Re: [PyMOL] get coordinates
Hi Bradley, If you have one of the latest builds, you can use this approach: http://www.mail-archive.com/pymol-users@lists.sourceforge.net/msg07754.html Hope it helps. Vitaly - Original Message - From: Bradley Hintze bradle...@aggiemail.usu.edu Date: Tuesday, July 20, 2010 5:37 pm Subject: [PyMOL] get coordinates To: pymol-users pymol-users@lists.sourceforge.net Hi all, Is there an easy way to get coordinates of a given atom? e.g. 'get_coordinates /model//A/ALA`76/CA' for the CA coordinates of resi 76 All the examples on the wiki use iterate to get the coordinates of a selection. Is there a simple way to get one coordinate of a given atom? -- Bradley J. Hintze Graduate Student Duke University School of Medicine 801-712-8799 -- This SF.net email is sponsored by Sprint What will you do first with EVO, the first 4G phone? Visit sprint.com/first -- http://p.sf.net/sfu/sprint-com-first ___ 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- us...@lists.sourceforge.net -- This SF.net email is sponsored by Sprint What will you do first with EVO, the first 4G phone? Visit sprint.com/first -- http://p.sf.net/sfu/sprint-com-first ___ 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] Label N-Glycosilation with Pymol
On Jul 19, 2010, at 12:29 PM, José Ignacio Sánchez Gallego wrote: Hi everybody, I have to make a 3D structure of my protein, I mutated some aminoacids in order to add some N-linked glycans, does anyone know is it possible to show the glycosilation on the surface of the 3D structure?? It would be a nice picture. Thanks in advance, Greetings Hi José, You can use GlyProt to *model* your glycan chains: http://www.glycosciences.de/modeling/glyprot/php/main.php HTH, Luca Luca Jovine, Ph.D. Group Leader EMBO Young Investigator Karolinska Institutet Department of Biosciences and Nutrition Center for Biosciences Hälsovägen 7, SE-141 57 Huddinge, Sweden Voice: +46.(0)8.6083-301 FAX: +46.(0)8.6081-501 E-mail: luca.jov...@ki.se W3: http://jovinelab.org -- This SF.net email is sponsored by Sprint What will you do first with EVO, the first 4G phone? Visit sprint.com/first -- http://p.sf.net/sfu/sprint-com-first ___ 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
[PyMOL] 3rd Call For Papers, 17th Annual Tcl/Tk Conference 2010
[[ Get your papers in. The deadline for abstracts and proposals is less than two weeks away. ]] 17th Annual Tcl/Tk Conference (Tcl'2010) http://www.tcl.tk/community/tcl2010/ October 11 - 15, 2010 Hilton Suites/Conference Center Chicago/Oakbrook Terrace, Illinois, USA Important Dates: Abstracts and proposals due August 1, 2010 Notification to authors August 15, 2010 WIP and BOF reservations open August 1, 2010 Author materials due October 1, 2010 Tutorials Start October 11, 2010 Conference starts October 13, 2010 Email Contact:tclconfere...@googlegroups.com Submission of Summaries Tcl/Tk 2010 will be held in Chicago/Oakbrook Terrace, Illinois USA from October 11 - 15, 2010. The program committee is asking for papers and presentation proposals from anyone using or developing with Tcl/Tk (and extensions). Past conferences have seen submissions covering a wide variety of topics including: * Scientific and engineering applications * Industrial controls * Distributed applications and Network Managment * Object oriented extensions to Tcl/Tk * New widgets for Tk * Simulation and application steering with Tcl/Tk * Tcl/Tk-centric operating environments * Tcl/Tk on small and embedded devices * Medical applications and visualization * Use of different programming paradigms in Tcl/Tk and proposals for new directions. * New areas of exploration for the Tcl/Tk language This year is the third year that the Tcl community is participating in the Google Summer of Code. The conference program committee would like to encourage submissions that report on the Tcl projects selected for Google SoC 2010. Submissions should consist of an abstract of about 100 words and a summary of not more than two pages, and should be sent as plain text to tclconference AT googlegroups DOT com no later than August 15, 2010. Authors of accepted abstracts will have until October 1, 2010 to submit their final paper for the inclusion in the conference proceedings. The proceedings will be made available on digital media, so extra materials such as presentation slides, code examples, code for extensions etc. are encouraged. Printed proceedings will be produced as an on-demand book at lulu.com The authors will have 25 minutes to present their paper at the conference. The program committee will review and evaluate papers according to the following criteria: * Quantity and quality of novel content * Relevance and interest to the Tcl/Tk community * Suitability of content for presentation at the conference Proposals may report on commercial or non-commercial systems, but those with only blatant marketing content will not be accepted. Application and experience papers need to strike a balance between background on the application domain and the relevance of Tcl/Tk to the application. Application and experience papers should clearly explain how the application or experience illustrates a novel use of Tcl/Tk, and what lessons the Tcl/Tk community can derive from the application or experience to apply to their own development efforts. Papers accompanied by non-disclosure agreements will be returned to the author(s) unread. All submissions are held in the highest confidentiality prior to publication in the Proceedings, both as a matter of policy and in accord with the U. S. Copyright Act of 1976. The primary author for each accepted paper will receive registration to the Technical Sessions portion of the conference at a reduced rate. Other Forms of Participation The program committee also welcomes proposals for panel discussions of up to 90 minutes. Proposals should include a list of confirmed panelists, a title and format, and a panel description with position statements from each panelist. Panels should have no more than four speakers, including the panel moderator, and should allow time for substantial interaction with attendees. Panels are not presentations of related research papers. Slots for Works-in-Progress (WIP) presentations and Birds-of-a-Feather sessions (BOFs) are available on a first-come, first-served basis starting in August 1, 2010. Specific instructions for reserving WIP and BOF time slots will be provided in the registration information available in June 2010. Some WIP and BOF time slots will be held open for on-site reservation. All attendees with an interesting work in progress should consider reserving a WIP slot. Registration Information More information on the conference is available the conference Web site (http://www.tcl.tk/community/tcl2010/) and will be published on various Tcl/Tk-related information channels. Reservations for hotel suites and $25 airport shuttle rides can be made at http://www.hilton.com/en/hi/groups/personalized/CHIOTHS-TCL-20101010/index.jhtml?WT.mc_id=POG To keep in touch with news regarding the conference and Tcl events in general, subscribe to the tcl-announce list. See:
