Hi Matt, > So some brief background, I am writing a pymol plugin for displaying > pharmacophores queries from ZincPharmer ( http://zincpharmer.csb.pitt.edu/), > which is developed in my lab. Version 1 of my plugin is available here: > http://sourceforge.net/projects/pharmer/files/ under the name load_query. > > Sorry if that quickly turned into an advertisement, but what I would like to
On the contrary, we welcome the promotion of PyMOL extensions! They help the community find resources we may not have known about and it helps the developer drive usage of his or her tools -- a win-win. In fact, the best way to promote a new script/plugin is to: (1) Create a PyMOLWiki webpage with example code, images, and links back to your own project page (if you have one) (2) Email the list an enticing advertisement for your new functionality Some people have even used PyMOLWiki page view counts in their grant applications to show usage. > be able to reproduce in pymol is something like this: > http://i.imgur.com/hiX2i.png . Where the wire mesh sphere's represent the > pharamacophores. Currently, I am using the cgo sphere's but they do not do > well when there are overlapping pharmacophores (a common case). We are planning on adding improved graphical and text annotations to PyMOL. So, while we cannot currently do what you want we hope to be able to in the near future. Last, I hesitate to suggest this because it's so unsightly, but if you need something in the meantime that resembles a mesh sphere (but is not exact) you can create your CGO spheres and then do, set cgo_debug, 1 No, it won't ray trace like that either -- they'll be converted to full spheres. Cheers, -- Jason > Hi Matt, > > There's currently no easy way to do this. Can you please send us some > screenshots of what you'd like to see implemented? > > Cheers, > > -- Jason > > On Tue, Oct 23, 2012 at 4:16 PM, Matthew Baumgartner <mp...@pitt.edu> wrote: > > Hi, > Is it now possible to have wire mesh cgo object spheres in pymol? > I found this thread from a while ago (2004) but googleing, I didn't > find anything more recent. > > > The one sort of work around that I though of was to create pseudo-atoms > and somehow modify their radius and then show them as mesh. > But I would like to use CGO objects if possible. > > Does anyone have any suggestions? > > Thanks, > Matt Baumgartner > > > > Sphere transparency example included below... > > ALPHA must preceed COLOR to be effective. > > PyMOL does not yet do a global sort of tranparent triangles, so there will > be artifacts in OpenGL. Raytracing should look fine however. > > # from within a .py OR .pym file... > > from pymol.cgo import * > from pymol import cmd > > obj = [ > > ALPHA, 1.0, > COLOR, 1.0, 1.0, 1.0, > SPHERE, 0.0, 0.0, 0.0, 0.5, > > ALPHA, 0.66, > COLOR, 1.0, 0.0, 0.0, > SPHERE, 1.0, 0.0, 0.0, 0.5, > > ALPHA, 0.33, > COLOR, 0.0, 1.0, 0.0, > SPHERE, 0.0, 1.0, 0.0, 0.5, > > ALPHA, 0.11, > COLOR, 0.0, 0.0, 1.0, > SPHERE, 0.0, 0.0, 1.0, 0.5, > ] > > cmd.load_cgo(obj,'cgo01') > > Cheers,war...@delanoscientific.com > Warren > > -- > Warren L. DeLano, Ph.D. > Principal Scientist > > . DeLano Scientific LLC > . 400 Oyster Point Blvd., Suite 213 > . South San Francisco, CA 94080 > . Biz:(650)-872-0942 Tech:(650)-872-0834 > . Fax:(650)-872-0273 Cell:(650)-346-1154 > . mailto:war...@delsci.com > > > -----Original Message----- > From: pymol-users-ad...@lists.sourceforge.net > [mailto:pymol-users-ad...@lists.sourceforge.net] On Behalf Of > Michael George Lerner > Sent: Wednesday, November 17, 2004 9:43 AM > To: pymol-users@lists.sourceforge.net > Subject: [PyMOL] wire-mesh spheres? > > > Hi, > > I want to draw a bunch of spheres of various sizes and > colors. I'm currently using cgos for this. No problem. > Now, I also want to draw wire-mesh spheres. Does anyone have > a script for making these? While I'm at it, is there a way > to make cgos transparent? > > Thanks, > > -Michael > > -- > This isn't a democracy;| _ |Michael Lerner > it's a cheer-ocracy. | ASCII ribbon campaign ( ) | Michigan > -Torrence, Bring It On| - against HTML email X | Biophysics > | / \ | mler...@umich > > > ------------------------------------------------------- > This SF.Net email is sponsored by: InterSystems CACHE FREE > OODBMS DOWNLOAD - A multidimensional database that combines > robust object and relational technologies, making it a > perfect match for Java, C++,COM, XML, ODBC and JDBC. > www.intersystems.com/match8 > _______________________________________________ > PyMOL-users mailing list > PyMOL-users@lists.sourceforge.net > https://lists.sourceforge.net/lists/listinfo/pymol-users > > > > ------------------------------------------------------------------------------ > Everyone hates slow websites. So do we. > Make your web apps faster with AppDynamics > Download AppDynamics Lite for free today: > http://p.sf.net/sfu/appdyn_sfd2d_oct > _______________________________________________ > 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 Schrödinger, Inc. (e) jason.vertr...@schrodinger.com (o) +1 (603) 374-7120 ------------------------------------------------------------------------------ Everyone hates slow websites. So do we. Make your web apps faster with AppDynamics Download AppDynamics Lite for free today: http://p.sf.net/sfu/appdyn_sfd2d_oct _______________________________________________ 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
