Konrad, There are several options for loading map data into PyMOL now:
XPLOR (format=xplor) CCP4 (format=ccpy) O/BRIX (format=brix) In addition, you can use the following non-crystallographic formats: Delphi/Grasp PHI files (format=phi) AVS FLD files (as output from MEAD) (format=fld) and in the current CVS, we have support for DX files output by APBS (format=dx). You can also bypass the file entirely and load an orthogonal "ChemPy brick" into PyMOL via NumPy. Example code for this can be found in examples/devel/brick01.py. Note that you must use a PyMOL build that included numeric Python in order for this to work (the RPMs and Linux binaries do not have it, so you may need to build from source using the _PYMOL_NUMPY define). There's also a "ChemPy Map" approach, which expects opaque packed C float data. Once in PyMOL, you can then use "isomesh" and "isosurface" to create mesh and solid isocontours. Or use "ramp_new" and "color" to color by the potential found in the map. Sorry about the lack of documentation -- it will improve. Cheers, Warren -- mailto:war...@delsci.com Warren L. DeLano, Ph.D. Principal Scientist DeLano Scientific LLC Voice (650)-346-1154 Fax (650)-593-4020 > -----Original Message----- > From: pymol-users-ad...@lists.sourceforge.net > [mailto:pymol-users-ad...@lists.sourceforge.net] On Behalf Of > Konrad Hinsen > Sent: Monday, June 21, 2004 7:10 AM > To: <pymol-users@lists.sourceforge.net> > <pymol-users@lists.sourceforge.net> > Subject: [PyMOL] Electronic density maps > > I am trying to visualize electronic densities that I prepare > in my own code. This means that I have to write them in XPlor > format in order to load them into PyMOL. Is there anywhere a > detailed description of that format, preferably with some > example files? The best I could find is a summary. > > Konrad. > -- > --------------------------------------------------------------------- > Konrad Hinsen > Laboratoire Léon Brillouin, CEA Saclay, > 91191 Gif-sur-Yvette Cedex, France > Tel.: +33-1 69 08 79 25 > Fax: +33-1 69 08 82 61 > E-Mail: hin...@llb.saclay.cea.fr > --------------------------------------------------------------------- > > > > ------------------------------------------------------- > This SF.Net email is sponsored by The 2004 JavaOne(SM) > Conference Learn from the experts at JavaOne(SM), Sun's > Worldwide Java Developer Conference, June 28 - July 1 at the > Moscone Center in San Francisco, CA REGISTER AND SAVE! > http://java.sun.com/javaone/sf Priority Code NWMGYKND > _______________________________________________ > PyMOL-users mailing list > PyMOL-users@lists.sourceforge.net > https://lists.sourceforge.net/lists/listinfo/pymol-users >
