RE: [PyMOL] Electrostatic potential maps in PyMOL
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
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
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
Re: [PyMOL] Electrostatic potential maps in PyMOL
There has been some talk on the list regarding failure of PyMOL in reading Delphi generated potential maps that I missed. I have generated phimap using a modified version of Delphi in the GRASP format that PyMOL reads and displays without any problem. So I am not sure what the problem is. Can anybody please let me know what was the problem with PyMOL reading Delphi generated GRASP potential maps? Was wondering if PyMOL is doing the right thing?? Thanks, Kaushik Raha Penn State University On Wednesday, July 9, 2003, at 10:48 AM, 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
Re: [PyMOL] Electrostatic potential maps in PyMOL
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 === On Wed, 9 Jul 2003, Kaushik Raha wrote: There has been some talk on the list regarding failure of PyMOL in reading Delphi generated potential maps that I missed. I have generated phimap using a modified version of Delphi in the GRASP format that PyMOL reads and displays without any problem. So I am not sure what the problem is. Can anybody please let me know what was the problem with PyMOL reading Delphi generated GRASP potential maps? Was wondering if PyMOL is doing the right thing?? Thanks, Kaushik Raha Penn State University On Wednesday, July 9, 2003, at 10:48 AM, 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)
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
