Re: [PyMOL] Reading CCP4 maps
One other thing - PyMOL has a flag which determines whether the density values will be normalised - if this flag is not set, then isomesh mesh_name, map_name, 1 will contour the map at 1-sigma; to contour at an absolute value, you must do set normalize_ccp4_maps=0 BEFORE loading the map. If the flag is set, the program will print some information about the calculated mean and std deviation when you load a map. Commonly-used settings like this can be put in your ~/.pymolrc file (at least on a UNIX system), so that they are executed whenever PyMOL starts up. Gareth --- Gareth Stockwell EMBL - European Bioinformatics Institute Wellcome Trust Genome Campus Hinxton Cambridge CB10 1SD gar...@ebi.ac.uk Tel 01223 492548 http://www.ebi.ac.uk/~gareth
Re: [PyMOL] Reading CCP4 maps
Quyen, * Quyen Hoang hoa...@mcmail.cis.mcmaster.ca [2002-09-05 15:32] wrote: I would like to read CCP4 electron-density maps into PyMol, but I don't know how (explore maps loaded fine). Would someone please give me a quick summary of the procedure. Thank you! simply doing: load mapfile.ccp4, map_object_name will load the map, but if the filename doesn't end in '.ccp4', then you'll need to specify that it is CCP4 format with something like: load mapfile.ccp4_map, map_object_name, 1, ccp4 Then you'll want to display it with a similar sort of isomesh command that you would have used for the xplor map. isomesh mesh_object_name, map_object_name, contour level, selection, radius The on-line manual describes this pretty clearly (in fact, probably better than I have!): http://pymol.sourceforge.net/html/S0400xtal.html Cheers, Robert -- Robert L. Campbell, Ph.D. http://biophysics.med.jhmi.edu/rlc r...@k2.med.jhmi.eduphone: 410-614-6313 Research Specialist/X-ray Facility Manager HHMI/Dept. of Biophysics Biophysical Chem., The Johns Hopkins University PGP Fingerprint: 9B49 3D3F A489 05DC B35C 8E33 F238 A8F5 F635 C0E2
Re: [PyMOL] Reading CCP4 maps
You can also type help load into either window for similar info. Nigel - Original Message - From: Robert Campbell r...@k2.med.jhmi.edu To: pymol-users@lists.sourceforge.net Sent: Thursday, September 05, 2002 12:47 PM Subject: Re: [PyMOL] Reading CCP4 maps Quyen, * Quyen Hoang hoa...@mcmail.cis.mcmaster.ca [2002-09-05 15:32] wrote: I would like to read CCP4 electron-density maps into PyMol, but I don't know how (explore maps loaded fine). Would someone please give me a quick summary of the procedure. Thank you! simply doing: load mapfile.ccp4, map_object_name will load the map, but if the filename doesn't end in '.ccp4', then you'll need to specify that it is CCP4 format with something like: load mapfile.ccp4_map, map_object_name, 1, ccp4 Then you'll want to display it with a similar sort of isomesh command that you would have used for the xplor map. isomesh mesh_object_name, map_object_name, contour level, selection, radius The on-line manual describes this pretty clearly (in fact, probably better than I have!): http://pymol.sourceforge.net/html/S0400xtal.html Cheers, Robert -- Robert L. Campbell, Ph.D. http://biophysics.med.jhmi.edu/rlc r...@k2.med.jhmi.eduphone: 410-614-6313 Research Specialist/X-ray Facility Manager HHMI/Dept. of Biophysics Biophysical Chem., The Johns Hopkins University PGP Fingerprint: 9B49 3D3F A489 05DC B35C 8E33 F238 A8F5 F635 C0E2 --- This sf.net email is sponsored by: OSDN - Tired of that same old cell phone? Get a new here for FREE! https://www.inphonic.com/r.asp?r=sourceforge1refcode1=vs3390 ___ PyMOL-users mailing list PyMOL-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/pymol-users
