Hi Paulo, Andreas - and other PyMOLers doing electrostatics
Sorry for the late reply - Our department is being relocated, and I've spent most of my time on that lately.... There was a problem with the posting, where some of the source code lines were wrapped. In most cases this was no problem, but in one line it is fatal: fprintf(outfile,"Map converted from MEAD AVS (fld) file "); The string in this line must be exactly 60 (sixty) characters long - there should be 22 spaces in the end. But I will strongly recommend that you use version 0.91 of PyMOL instead, as this reads the .fld maps from MEAD directly without the need for conversion. Furthermore, it reads maps of any size, not just 65x65x65. v0.91 is still only available from CVS, but maybe we can convince Warren to make an official release soon :-) Best regards Esben -----Original Message----- From: Paulo Martel To: EPF (Esben Peter Friis) Sent: 14-09-03 20:28 Subject: Re: [PyMOL] Electrostatic potential maps in PyMOL Dear Esben, no matter how hard I try, I cannot make pymol read a phi map converted from avs with your utility. The .fld file was generated with the potential program in the latest MEAD distribution and converted with problems to .phi (the values output by fld2phi seem normal). When I try to load the grid into pymol, it displays and absurdly big range like it was read the numbers in the wrong endianess. I am using pymol 0.90 on a RedHat 7.3 PIV Linux system, and compiled your program with gcc. Best regards, Paulo On Wed, 2003-07-09 at 15:48, 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 object name of the surface (choose whatever you want), > "map" is the object name of the electrostatic potential map and the number > is the contour level. The commands isomesh and isodot have the same syntax > and do exactly what you think. > > > > Best regards (and please forgive me for quoting source code here :) > > Esben > > > ************************************************************** > * Source code for fld2phi * > * save as: fld2phi.c * > * compile with: gcc -o fld2phi fld2phi.c * > ************************************************************** > > /* This is fld2phi.c */ > /* This program reads little-endian AVS fields (.fld-files) from MEAD and > */ > /* convert it to big-endian .phi maps readable by PyMOL > */ > /* Tested on i386-Linux only */ > /* (c) Esben Friis, 2003 */ > > /* ------------ INCLUDES --------------- */ > > #include <stdio.h> > #include <stdlib.h> > > /* ------------- DEFINES --------------- */ > > #define VERSION "1.0" > #define DATE "2003-07-09" > > /* ------------- FUNCTIONS ------------- */ > > int get_fld_header (char *filename, int *gridpts, float *xmin, float *ymin, > float *zmin, float *xmax, float *ymax, float *zmax ) > { > char buffer[256]; > int i; > FILE *infile; > > if (!(infile = fopen(filename,"rb"))) > return 0; > else > { > for (i=0; i<4; i++) > fgets(buffer, 256, infile); > > fgets(buffer, 256, infile); > *gridpts = atoi(buffer+5); /* the number of grid points in each > direction */ > > for (i=0; i<5; i++) > fgets(buffer, 256, infile); > > fgets(buffer, 256, infile); /* min extent line */ > sscanf(buffer+8, "%f %f %f", xmin, ymin, zmin); > > fgets(buffer, 256, infile); /* max extent line */ > sscanf(buffer+8, "%f %f %f", xmax, ymax, zmax); > > fgets(buffer, 256, infile); > > fclose (infile); > > return 1; > } > } > > > int get_fld_grid (char *filename, int gridpts, float *grid) > { > char buffer[256]; > int i, x, y, z, nobj; > FILE *infile; > > if (!(infile = fopen(filename,"rb"))) > return 0; > else > { > for (i=0; i<13; i++) > fgets(buffer, 256, infile); > > /* --- end of header ---- */ > > fgets(buffer, 3, infile); /* junk bytes */ > nobj = fread(grid, 4, gridpts*gridpts*gridpts, infile); /* data array > */ > > printf ("read %d data points from %s\n", nobj, filename); > > fclose (infile); > } > } > > > void write_big_endian_float(FILE *stream, float *f) > { > char *p; > char rev[4]; > > p = (char*) f; > rev[0] = p[3]; > rev[1] = p[2]; > rev[2] = p[1]; > rev[3] = p[0]; > fwrite(&rev, 4, 1, stream); > } > > > int write_phi(char *filename, int gridpts, float *grid, float xmin, float > ymin, float zmin, float xmax, float ymax, float zmax) > { > float xmid, ymid, zmid, scale; > FILE *outfile; > int i, x, y,z; > > if (!(outfile = fopen(filename,"wb"))) > return 0; > else > { > > xmid = (xmax+xmin)/2.0; > ymid = (ymax+ymin)/2.0; > zmid = (zmax+zmin)/2.0; > > scale = ((float)gridpts-1.0)/(xmax-xmin); > > printf ("midpoint %f, %f, %f, scale = %f\n", xmid, ymid, zmid, scale); > > fprintf(outfile,"%c%c%c%c",0,0,0,0x14); > fprintf(outfile,"now starting phimap "); > fprintf(outfile,"%c%c%c%c",0,0,0,0x14); > fprintf(outfile,"%c%c%c%c",0,0,0,0x46); > fprintf(outfile,"potential "); > fprintnverted f(outfile,"Map cofrom MEAD AVS (fld) file > "); > fprintf(outfile,"%c%c%c%c",0,0,0,0x46); > fprintf(outfile,"%c%c%c%c",0,0x10,0xc3,0x04); > > /* order is z y x */ > for (z=0; z<gridpts; z++) > for (y=0; y<gridpts; y++) > for (x=0; x<gridpts; x++) > write_big_endian_float(outfile, > grid+gridpts*gridpts*z+gridpts*y+x); > > > fprintf(outfile,"%c%c%c%c%c%c%c%c",0x13,0x80,0x00,0x10,0xc3,0x04,0x00,0x 00); > > fprintf(outfile," end of phimap "); > > fprintf(outfile,"%c%c%c%c",0x10,0,0,0); > fprintf(outfile,"%c%c%c%c",0x10,0,0,0); > > write_big_endian_float(outfile, &scale); > write_big_endian_float(outfile, &xmid); > write_big_endian_float(outfile, &ymid); > write_big_endian_float(outfile, &zmid); > fprintf(outfile,"%c%c%c%c",0x10,0,0,0); > > fclose(outfile); > } > } > > void usage(void) > { > fprintf(stderr,"USAGE:\n"); > fprintf(stderr,"fld2phi <map.fld> <map.phi>\n\n"); > fprintf(stderr,"Converts an AVS .fld grid file <map.fld> written by > MEAD's 'potential'\n"); > fprintf(stderr,"program to a big-endian Delphi grid file <map.phi> which > is readable\n"); > fprintf(stderr,"by eg. PyMOL.\n"); > fprintf(stderr,"Notice that PyMOL (v0.90) can only handle grids of > 65x65x65 points.\n"); > fprintf(stderr,"fld2phi is version %s from %s\n",VERSION,DATE); > > exit(0); > } > > int main (int argc, char **argv) > { > float xmin, ymin, zmin, xmax, ymax, zmax; > float *grid; > int gridpts; > > if (argc !=3) > usage(); > > get_fld_header(argv[1], &gridpts, &xmin, &ymin, &zmin, &xmax, &ymax, > &zmax); > > printf ("%d, %f, %f, %f, %f, %f, %f\n", gridpts, xmin, ymin, zmin, xmax, > ymax, zmax); > > printf ("Grid size is %d.\n", gridpts); > if (gridpts != 65) > { > printf ("WARNING:\n"); > printf ("PyMOL version 0.90 only reads maps which are 65x65x65!\n"); > } > > grid = (float*) malloc(gridpts*gridpts*gridpts*4); > > get_fld_grid(argv[1], gridpts, grid); > > write_phi(argv[2], gridpts, grid, xmin, ymin, zmin, xmax, ymax, zmax); > > return 0; > } > > > ------------------------------------------------------- > 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 > -- Paulo Martel Dept. de Química e Bioquímica Faculdade de Ciências e Tecnologia Universidade do Algarve Campus de Gambelas, 8000-117 FARO Tel: 289800900 Ext.7402
