From: Mark A. White <[email protected]> To: John Bruning <[email protected]> Cc: [email protected] <[email protected]> Subject: Re: [ccp4bb] .phs file conversion Date: Wed, 4 Mar 2009 14:16:47 -0600
John, The PHS file has the coefficients to make a map, along with the cell parameters, but is not itself a map. There are a few choices. 1) View the PHS file in XtalView (xfit) or MIFit, which is where it was meant to be viewed. COOT will also display maps from PHS files. The PDB file must have the correct CRYST1 entry. Xfit has an output option to save the map coefficients as an MTZ file. This requires a working CCP4 installation. 2) Use CCP4 to convert the PHS file into an MTZ and then to a CCP4 MAP, using FFT. This can then be viewed in PYMOL. ############################################################################## # Convert LSCALE.PHS file to MTZ ############################################################################## f2mtz HKLIN pmb_lscale.phs HKLOUT pmb_lscale.mtz << f2mtz_eof > f2mtz.html TITLE MTZ from PHSS From FoFc_calc.inp -> pmb_cns2phs.pl PNAME D999 DNAME D999 CELL 86.15 72.65 25.89 90.00 90.00 90.00 LABOUT H K L FO FC PHIC CTYPout H H H F F P FORMAT '(2X,3F5.0,3F10.3)' SYMM 18 f2mtz_eof # Note that the format of the PHS file is not standardized, but that F2MTZ requires a well defined fixed format. Good luck, Mark On Wed, 2009-03-04 at 13:48 -0600, John Bruning wrote: > Hi, > > I have a .phs file with map coefficients that I would like to open in > pymol. So, I would like to convert the file to either a ccp4 or cns > map file, or a file format that pymol will recognize. I do not have > an .mtz file with the same map coefficients included. Can anyone help > me? > > > Thanks, > John Yours sincerely, Mark A. White, Ph.D. Assistant Professor, Dept. Biochemistry and Molecular Biology, Manager, Sealy Center for Structural Biology and Molecular Biophysics X-ray Crystallography Laboratory, Basic Science Building, Room 6.660 C University of Texas Medical Branch Galveston, TX 77555-0647 Tel. (409) 747-4747 Cell. (409) 539-9138 Fax. (409) 747-4745 mailto://[email protected] http://xray.utmb.edu http://xray.utmb.edu/~white Yours sincerely, Mark A. White, Ph.D. Assistant Professor, Dept. Biochemistry and Molecular Biology, Manager, Sealy Center for Structural Biology and Molecular Biophysics X-ray Crystallography Laboratory, Basic Science Building, Room 6.660 C University of Texas Medical Branch Galveston, TX 77555-0647 Tel. (409) 747-4747 Cell. (409) 539-9138 Fax. (409) 747-4745 mailto://[email protected] http://xray.utmb.edu http://xray.utmb.edu/~white
