[PyMOL] New script: spectrumany
Hi pymol users, there is a new script on the wiki that does arbitrary gradient coloring, it's called "spectrumany". http://pymolwiki.org/index.php/Spectrumany Cheers, Thomas -- 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] draw vector
Bradley, set dash_gap, 0, distName where distName is the name of the distance object from the distance command. Cheers, -- Jason On Thu, Jul 22, 2010 at 2:02 PM, Bradley Hintze wrote: > I have measurements in my figure so set dash_gap, 0 is not desirable > (unless i can specify a particular object??) > I tried looking at CGO but all I can find on the wiki is how to draw > text and circles. Is there a page I'm not seeing that explaining > cmd.load_cgo in detail?? > > On Thu, Jul 22, 2010 at 12:22 PM, Jason Vertrees > wrote: >> Bradley, >> >> The fastest way is to create two pseudoatoms and measure the distance >> between them. For an arrow, see Modevectors >> (http://www.pymolwiki.org/index.php/Modevectors). >> >> pseudoatom pt1, pos=[x1, y1, z1] >> pseudoatom pt2, pos=[x2, y2, z2] >> distance /pt1, /pt2 >> set dash_gap, 0 >> >> You can also create CGO lines between two points, if you want. >> >> Cheers, >> >> -- Jason >> >> On Thu, Jul 22, 2010 at 11:58 AM, Bradley Hintze >> wrote: >>> Hi all, >>> >>> Can I draw a vector if I give two XYZ coords in pymol? >>> >>> e.g. >>> draw_vector(x1, y1, z1, x2, y2, z2) >>> >>> Thanks, >>> Bradley >>> >>> -- >>> 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 >> > > > > -- > Bradley J. Hintze > Graduate Student > Duke University > School of Medicine > 801-712-8799 > -- 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
Re: [PyMOL] draw vector
I have measurements in my figure so set dash_gap, 0 is not desirable (unless i can specify a particular object??) I tried looking at CGO but all I can find on the wiki is how to draw text and circles. Is there a page I'm not seeing that explaining cmd.load_cgo in detail?? On Thu, Jul 22, 2010 at 12:22 PM, Jason Vertrees wrote: > Bradley, > > The fastest way is to create two pseudoatoms and measure the distance > between them. For an arrow, see Modevectors > (http://www.pymolwiki.org/index.php/Modevectors). > > pseudoatom pt1, pos=[x1, y1, z1] > pseudoatom pt2, pos=[x2, y2, z2] > distance /pt1, /pt2 > set dash_gap, 0 > > You can also create CGO lines between two points, if you want. > > Cheers, > > -- Jason > > On Thu, Jul 22, 2010 at 11:58 AM, Bradley Hintze > wrote: >> Hi all, >> >> Can I draw a vector if I give two XYZ coords in pymol? >> >> e.g. >> draw_vector(x1, y1, z1, x2, y2, z2) >> >> Thanks, >> Bradley >> >> -- >> 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 > -- 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] draw vector
Bradley, The fastest way is to create two pseudoatoms and measure the distance between them. For an arrow, see Modevectors (http://www.pymolwiki.org/index.php/Modevectors). pseudoatom pt1, pos=[x1, y1, z1] pseudoatom pt2, pos=[x2, y2, z2] distance /pt1, /pt2 set dash_gap, 0 You can also create CGO lines between two points, if you want. Cheers, -- Jason On Thu, Jul 22, 2010 at 11:58 AM, Bradley Hintze wrote: > Hi all, > > Can I draw a vector if I give two XYZ coords in pymol? > > e.g. > draw_vector(x1, y1, z1, x2, y2, z2) > > Thanks, > Bradley > > -- > 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] draw vector
Hi all, Can I draw a vector if I give two XYZ coords in pymol? e.g. draw_vector(x1, y1, z1, x2, y2, z2) Thanks, Bradley -- 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] Fwd: Help setting apbs tools2 on Mac
Hi Daniel, The version on the wiki (http://pymolwiki.org/index.php/User:Mglerner) should handle the fink (apbs-mpi-openmpi and apbs-mpi-lammpi) and macports (apbs-mpi) versions of MPI-enabled APBS. Please note that the PyMOL-APBS plugin doesn't go out of its way to take advantage of parallel features; it just calls the MPI-enabled versions of APBS. Because I test the non-parallel versions more frequently, it checks for the normal APBS first. If you want it to find the MPI by default, you can 1) uninstall the non-MPI version, 2) set the APBS_BINARY variable in the plugin directly, or 3) set the APBS_BINARY_DIR environment variable. It's worth noting that the environment variables weren't working in some previous versions of the plugin. Cheers, -Michael On Wed, Jul 21, 2010 at 2:56 PM, Michael Lerner < mglerner+sourcefo...@gmail.com > wrote: > Hi Daniel, > > Sorry for the delay! I wasn't actually aware of that talk page; you'll get > a faster response if you email the PyMOL list. > > The version that you can download from pymolwiki.org will fix the problems > you had with the temp path. I've never used the openmpi version of APBS on > the mac before, so I want to do a few more tests before I put up a version > of the plugin that finds it by default. In the meantime, you can type the > binary location into the APBS Location box and it should work. You don't > need to worry about APBS's psize.py for the vast majority of systems. > > I'll let you know when I've updated the plugin fully deal with this. > > Note that the plugin will still run things using the same input files it > would with a single-processor APBS. > > -Michael > > > On Tue, Jul 20, 2010 at 7:15 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 >> 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)? >> [ snip ] > > -- Michael Lerner, Ph.D. IRTA Postdoctoral Fellow Laboratory of Computational Biology NIH/NHLBI 5635 Fishers Lane, Room T909, MSC 9314 Rockville, MD 20852 (UPS/FedEx/Reality) Bethesda MD 20892-9314 (USPS) -- 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
