RE: [PyMOL] Electrostatic potential maps in PyMOL
Thanks everybody for suggestiones, and Warren for fixing the problem. I will see if we could generate some phimap not 65x65x65. Ksushik, I don't know why your Delphi is working fine, here is my output from load phimap, which it should be cause of the endianess: PHIMapToStr: now starting phimap PHIMapToStr: potential PHIMapToStr: qdiffxas: qdiffxs4 with an improved surfacing routine PHIMapToStr: j# ObjectMap: Map Read. Range = -3388. to 37 Crystal: Unit Cell1.0001.0001.000 Crystal: Alpha Beta Gamma90.000 90.000 90.000 Crystal: RealToFrac Matrix Crystal:1.0.0. Crystal:0.1.0. Crystal:0.0.1. Crystal: FracToReal Matrix Crystal:1.0.0. Crystal:0.1.0. Crystal:0.0.1. Crystal: Unit Cell Volume1. Executive: object map created. Best Yu === Yu Chen Howard Hughes Medical Institute Chemistry Building, Rm 122 University of Maryland at Baltimore County 1000 Hilltop Circle Baltimore, MD 21250 phone: (410)455-6347 (410)455-2718 fax:(410)455-1174 email: c...@hhmi.umbc.edu === On Wed, 9 Jul 2003, Warren L. DeLano wrote: Okay, scratch that -- I fixed the problem, relying on standard Fortran unformatted IO conventions to automatically determine endianness and map size. PyMOL should now be able to read a PHI map of any dimensionality, so long as record size is implicitly and correctly specified in the map file. This may or may not be the case for .phi files written from C (for example, fld2phi is hard-coded for a 65x65x65 map, because the data block's record length specifier is hardcoded to be 0x10c304 = 65*65*65*4). Can someone send me a PHI map which is not 65x65x65 for testing purposes? Please include the associated PDB file for visual verification. Thanks! Looks like we'll need to push out another release sooner rather than later... Cheers, Warren -- mailto:war...@delanoscientific.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 Warren L. DeLano Sent: Wednesday, July 09, 2003 2:20 PM To: 'EPF (Esben Peter Friis)'; 'Kaushik Raha '; 'Yu Chen ' Cc: pymol-users@lists.sourceforge.net Subject: RE: [PyMOL] Electrostatic potential maps in PyMOL Yes, you have identified the problem: PyMOL 0.90 currently only reads PHI files in one of the two endian formats (not sure if it is big or little). The problem is, how it PyMOL to determine which format the incoming map is in? The file format is so darn implicit, I haven't yet come up with any effective way of doing it without risking a floating exception on finicky hardware. Any ideas? If we can just determine the enddian-ness of the incoming file, then the rest is a snap. Warren -- mailto:war...@delanoscientific.com Warren L. DeLano, Ph.D. Principal Scientist DeLano Scientific LLC Voice (650)-346-1154 Fax (650)-593-4020 --- This SF.Net email sponsored by: Parasoft Error proof Web apps, automate testing more. Download eval WebKing and get a free book. www.parasoft.com/bulletproofapps ___ PyMOL-users mailing list PyMOL-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/pymol-users
Re: [PyMOL] Electrostatic potential maps in PyMOL
Yu Chen, I think it is because of endianess. My phi files were generated by Delphi on an SGI in the GRASP format. My PyMOL 088 on Linux does not seem to mind it. I think Warren has fixed the problem of endianess and it should be fine in the next release. Kaushik. On Thursday, July 10, 2003, at 10:11 AM, Yu Chen wrote: Thanks everybody for suggestiones, and Warren for fixing the problem. I will see if we could generate some phimap not 65x65x65. Ksushik, I don't know why your Delphi is working fine, here is my output from load phimap, which it should be cause of the endianess: PHIMapToStr: now starting phimap PHIMapToStr: potential PHIMapToStr: qdiffxas: qdiffxs4 with an improved surfacing routine PHIMapToStr: j# ObjectMap: Map Read. Range = -3388. to 37 Crystal: Unit Cell1.0001.0001.000 Crystal: Alpha Beta Gamma90.000 90.000 90.000 Crystal: RealToFrac Matrix Crystal:1.0.0. Crystal:0.1.0. Crystal:0.0.1. Crystal: FracToReal Matrix Crystal:1.0.0. Crystal:0.1.0. Crystal:0.0.1. Crystal: Unit Cell Volume1. Executive: object map created. Best Yu === Yu Chen Howard Hughes Medical Institute Chemistry Building, Rm 122 University of Maryland at Baltimore County 1000 Hilltop Circle Baltimore, MD 21250 phone: (410)455-6347 (410)455-2718 fax:(410)455-1174 email: c...@hhmi.umbc.edu === On Wed, 9 Jul 2003, Warren L. DeLano wrote: Okay, scratch that -- I fixed the problem, relying on standard Fortran unformatted IO conventions to automatically determine endianness and map size. PyMOL should now be able to read a PHI map of any dimensionality, so long as record size is implicitly and correctly specified in the map file. This may or may not be the case for .phi files written from C (for example, fld2phi is hard-coded for a 65x65x65 map, because the data block's record length specifier is hardcoded to be 0x10c304 = 65*65*65*4). Can someone send me a PHI map which is not 65x65x65 for testing purposes? Please include the associated PDB file for visual verification. Thanks! Looks like we'll need to push out another release sooner rather than later... Cheers, Warren -- mailto:war...@delanoscientific.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 Warren L. DeLano Sent: Wednesday, July 09, 2003 2:20 PM To: 'EPF (Esben Peter Friis)'; 'Kaushik Raha '; 'Yu Chen ' Cc: pymol-users@lists.sourceforge.net Subject: RE: [PyMOL] Electrostatic potential maps in PyMOL Yes, you have identified the problem: PyMOL 0.90 currently only reads PHI files in one of the two endian formats (not sure if it is big or little). The problem is, how it PyMOL to determine which format the incoming map is in? The file format is so darn implicit, I haven't yet come up with any effective way of doing it without risking a floating exception on finicky hardware. Any ideas? If we can just determine the enddian-ness of the incoming file, then the rest is a snap. Warren -- mailto:war...@delanoscientific.com Warren L. DeLano, Ph.D. Principal Scientist DeLano Scientific LLC Voice (650)-346-1154 Fax (650)-593-4020 --- This SF.Net email sponsored by: Parasoft Error proof Web apps, automate testing more. Download eval WebKing and get a free book. www.parasoft.com/bulletproofapps ___ PyMOL-users mailing list PyMOL-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/pymol-users
[PyMOL] New Map Formats Coming...
PyMOLers, In response to user requests, I have added support for BRIX (O maps) and FLD (AVS Field) map formats in the current development version. Are there any other map formats which people would use heavily if PyMOL were able to support them? Thanks, Warren -- mailto:war...@delanoscientific.com Warren L. DeLano, Ph.D. Principal Scientist DeLano Scientific LLC Voice (650)-346-1154 Fax (650)-593-4020
Re: [PyMOL] Electrostatic potential maps in PyMOL
Hi Esben, I tried to follow your instructions to create and display an electrostatic surface potential. I used 1UBQ.pdb as input. In Mead, I encountered the following error when running potential -epsin 2 -CoarseFieldOut 1UBQ 1UBQ Starting potential for molecule named 1UBQ with interior dielectric constant = 2 using the following physical conditions: Exterior dielectric constant, espext = 80 Solvent probe radius, solrad = 1.4 Ion exclusion layer thickness, sterln = 2 Temperature, T = 300 Ionic strength, ionicstr = 0 Hueckel factor (epsext*kappasq) = 0 ln(10) * kBolt * T = 0.00413391 kBolt = 5.98444e-06 conconv = 0.000602214 econv = 331.842 Bohr radius = 0.529177 Proton Charge = 1 No blab level set (so no blabbing) INPUT FAILURE in FinDiffMethodRep::read from file1UBQ.ogmbad Coord-type entry No fld file is created. Any suggestion? The calculation was run on a PIII Xeon linux box. Thanks Andreas On Wed, 2003-07-09 at 08:48, EPF (Esben Peter Friis) wrote: Hi PyMOL users, MEAD's potential maps can be used in PyMOL, but it requires a little more than a bit of tweaking, as the maps are in the AVS .fld format, which can not be read by PyMOL. (These maps can be read by Dino, as Paulo just mentioned). Also, PyMOL reads (as far as I can see) only big-endian phi-maps. I have written a small program, which does the conversion from .fld to big-endian-.phi, so the maps can be read by PyMOL. It just finished it today, and it has only been tested on Linux (i386), so beware ;-) To create a nice electrostatic surface, you need: * Gromacs (not strictly necessary, but makes life easier) Download from http://www.gromacs.org * MEAD. Download from http://www.scripps.edu/bashford/ * fld2phi, source code quoted below (sorry, but I don't have access to our external web server, and it's only about 4kb). * PyMOL, of course (v0.88 or newer). Here is an example how to create everything from scratch for 4PTI.pdb Gromacs steps - 1) use pdb2gmx to create .gro and .top files: pdb2gmx -f 4PTI.pdb -o 4PTI.gro -p 4PTI.top 2) use grompp to create .tpr file: grompp -f 4PTI.mdp -p 4PTI.top -o 4PTI.tpr -c 4PTI.gro The file 4PTI.mdp contains the parameters for the Gromacs simulation. But as we are not going to do any simulation this time, an empty file is ok. It can be created with touch 4PTI.mdp. 3) use editconf to create a MEAD-readable pdb file: editconf -f 4PTI.tpr -mead -o 4PTI.pqr.pdb The output pdb file must then be renamed to be recognized by MEAD: mv 4PTI.pqr.pdb 4PTI.pqr MEAD steps -- 1) create a .ogm file which specifies the grid size. Notice that PyMOL can only handle grids which are 65x65x65 points, so your only option is to change the spacing between points. You can specify focussing options in the .ogm file, but only the coarsest grid is written anyway, so you only need one line in the 4PTI.ogm file: ON_GEOM_CENT 65 1.0 See documentation for other centering options (first parameter). Next number is the number of grid points on each side (must be 65 to be readable by PyMOL). The last number is a real specifying the distance between grid points. 2) Run 'potential' to create the grid: potential -epsin 2 -CoarseFieldOut 4PTI 4PTI The epsin option is mandatory and specifies the internal (in the protein) dielectric constant. The program will say something like: WARINING from potential main program: Could not open field point file, 4PTI.fpt, for reading. Exiting without giving any potentials. This can be ignored. The program still writes out a 4PTI.fld file with the grid. Notice that this file in not overwritten, so you must delete it manually if it already exists. Convert to PyMOL readable grid -- 1) Use the fld2phi to convert the .fld file to a big-endian .phi grid file: fld2phi 4PTI.fld 4PTI.phi This sould create a 4PTI.phi file which is readable by PyMOL. PyMOL steps --- 1) Load the structure including the hydrogens built by Gromacs: load 4PTI.pqr, 4PTI 2) Create a selection of the water: select water, 4PTI and resn SOL 3) Remove the water atoms: remove water 4) Show the surface of the 4PTI object: show surface, 4PTI 5) Load the electrostatic grid: load 4PTI.phi, map You can show the extent of the grid box by clicking on the object called map in the object list to the right. 6) Create a color ramp object: ramp_new e_lvl, map, [-0.02,0.00,0.02] 7) Color the surface according to the grid and map: set surface_color, e_lvl, 4PTI Thats it. You can change the color scale on the fly by issuing another ramp_new command with other numbers. The 3 numbers are red-point, white-point and blue-point, respectively. The scale can also be changed by ctrl+mid-click while you drag the color scale. It is also possible to create one or more contour surfaces: isosurface contour1, map, -0.05 where contour1 is the
