Hi! As far as I can see from the pymol source code, the Phimap loading routine requires the map to be big-endian (also on little-endian hardware). I guess this means that maps from SGI versions of Delphi or from GRASP (which only runs on SGI) works fine, but maps created with Linux (i386 or other little-endian machines) versions of DelPhi does not work. You would typically see enourmous ranges, as Yu reports.
Another matter - I go for MEAD because it is GPL. Neither Grasp or Delphi is free - and Grasp only runs on SGI. Cheers, Esben ---Original Message----- From: Kaushik Raha To: Yu Chen Cc: pymol-users@lists.sourceforge.net Sent: 09-07-03 22:42 Subject: Re: [PyMOL] Electrostatic potential maps in PyMOL Yu Chen, I have attached the output from the load command (which loads the phimap). I don't see the error that you describe. Does this output mean that it is working fine? I can generate a surface and color it with the electrostatic potential too. But I am not sure if I can trust the results since there is no gradient in the colors. It is either red or blue. Unfortunately I cant compare it to GRASP since we don't have that in our lab. Anyway let me know. Kaushik. PHIMapToStr: now starting phimap PHIMapToStr: potential PHIMapToStr: qdiffxas: qdiffxs4 with an improved surfacing routine PHIMapToStr: end of phimap Crystal: Unit Cell 1.000 1.000 1.000 Crystal: Alpha Beta Gamma 90.000 90.000 90.000 Crystal: RealToFrac Matrix Crystal: 1.0000 0.0000 0.0000 Crystal: 0.0000 1.0000 0.0000 Crystal: 0.0000 0.0000 1.0000 Crystal: FracToReal Matrix Crystal: 1.0000 0.0000 0.0000 Crystal: 0.0000 1.0000 0.0000 Crystal: 0.0000 0.0000 1.0000 Crystal: Unit Cell Volume 1. Executive: object "map" created. On Wednesday, July 9, 2003, at 03:58 PM, Yu Chen wrote: > Hello, Kaushik > > Yeah, we do had problems with DelPhi to PyMoL. I don't know what your > mean by "modified version of Delphi..." We bought the latest Delphi > from > their website, and used the data from all the example folders comes > with > Delphi. The calculation all went well. When we tried to read the phimap > into PyMoL, > > after > load delphi-map.phi, e_pot > > In the console window, the line > objectMap: Map Read. Range= -....... to ...... > > Then range is incredibly large, the negtive and positive values each > has > about over 30 digits! > > But when we use the same data in GRASP to generate the phimap, it > reads in > well. If you could give us some advice on how you modified Delphi, or > how > to get it, we would be greatly appreciate! > > Best > Yu Chen > > =========================================== > Yu Chen > Howard Hughes Medical Institute > Chemistry Building, Rm 122 > University of Maryland at Baltimore County > 1000 Hilltop Circle > Baltimore, MD 21250 > email: c...@hhmi.umbc.edu > ===========================================
