-----BEGIN PGP SIGNED MESSAGE----- Hash: SHA1 Dear Eric,
in order to get sf_convert running, you can of course run it within a csh-environment which is most likely installed on your system. CCP4 provides the setup-script also in csh-syntax ($CBIN/ccp4.setup-csh for the binary installation), this ought to overcome your errors. Since Phenix.model_vs_data requires a PDB file anyhow, phenix could check if the data file is CIF or mmCIF, then check if the symmetry information is present and if not use the one from the PDB file. If you send your request to the Phenix developers, they probably implement this in no time. Best, Tim On 03/26/2014 02:28 PM, Eric Williams wrote: > Thanks for the suggestion, Tim. :) Someone responded off-list with > a similar suggestion. Another suggestion was to download the MTZ > from PDB_REDO. These solutions would be great if I only needed one > set (or perhaps a handful of sets) of structure factors in MTZ > format. Since that's not the case, I should explain the context of > my question. > > I've been trying to run Phenix.model_vs_data on the whole PDB. That > program requires MTZ format, but the PDB supplies structure factors > in mmCIF format. I've tried (with multiple versions of Phenix) to > use Phenix.cif_as_mtz to perform the conversions, but that's been a > less than satisfying experience. It runs rather slowly, and for > reasons I haven't yet deciphered, it fails to convert in about 50% > of cases. It's not clear to me how much of the problem is rooted in > the program vs. my own mistakes. Regardless, I can't afford to lose > more time fighting with cif_as_mtz, so I decided to try > sf_convert. > > My understanding is that sf_convert is basically a wrapper for > cif2mtz when MTZ is selected as the target format. In theory it's a > very convenient wrapper, since it can take PDB model files as > additional input to find cell and symmetry information that may be > lacking in mmCIF structure factor files. I'm sure I could write a > wrapper script of my own, but I was trying to avoid reinventing the > wheel. > > Eric > > > On Wed, Mar 26, 2014 at 5:51 AM, Tim Gruene > <t...@shelx.uni-ac.gwdg.de> wrote: > > Dear Eric, > > I usually use cif2mtz from CCP4 to import structure factor files > from the PDB into mtz. Works excellently. > > I assume that for some reason sf_convert expects your CCP4 setup > file to be the csh version but finds the POSIX sh version, hence > the error messages. On my system I get the error message '/bin/csh: > not found'. > > csh is [flame] deprecated and [/flame] not following the POSIX > standard, so the old scripts cause trouble on modern systems which > are mostly based on bash, or ksh, or zsh, or any other of these > variants, all of are sh-compatible. The best solution to your > problem is to use cif2mtz, and the best answer to your question > would be the author of sf_convert to modernise the program. > > Best, Tim > > On 03/26/2014 05:00 AM, Eric Williams wrote: >>>> Does anyone here have experience running sf_convert? I know >>>> it's not part of CCP4, but it does rely on CCP4 for >>>> converting structure factors to MTZ format. >>>> >>>> When I try to run it, I get errors that suggest that my shell >>>> isn't bash, but it really is. The program output is as >>>> follows. >>>> >>>> sf_convert -o MTZ -sf 2hr0-sf.cif -pdb 2hr0.pdb -out >>>> 2hr0-sf.mtz >>>> >>>> Input file FORMAT=MMCIF Data type is Amplitude (F). If the >>>> guessed input format (MMCIF) is wrong, please use command: >>>> sf_convert -i input_format -o output_format -sf data_file >>>> >>>> Input File Name = 2hr0-sf.cif : (format=MMCIF) Doing mmcif to >>>> mmcif conversion.. Number of data blocks = 1 >>>> Data_block_id=r2hr0sf, pdbid=2hr0 Converting to mtz .. >>>> export: Command not found. export: Command not found. export: >>>> Command not found. export: Command not found. >>>> ccp4_first_in_path=1: Command not found. export: Command not >>>> found. export: Command not found. export: Command not found. >>>> export: Command not found. if: Expression Syntax. >>>> >>>> Output File Name = 2hr0-sf.mtz : (MTZ format) >>>> >>>> No output file is produced. I recognize some of the output >>>> from ccp4-setup.sh, but I don't know what's going wrong. >>>> Ideas? Suggestions? >>>> >>>> Eric >>>> > >> > - -- - -- Dr Tim Gruene Institut fuer anorganische Chemie Tammannstr. 4 D-37077 Goettingen GPG Key ID = A46BEE1A -----BEGIN PGP SIGNATURE----- Version: GnuPG v1.4.12 (GNU/Linux) Comment: Using GnuPG with Icedove - http://www.enigmail.net/ iD8DBQFTMuQKUxlJ7aRr7hoRAuJ7AKCSr4ec23Z3eLk6bZQYGLbAfpqADQCfQWo6 epegoqZIaG2yuJe/KHjy9eU= =ft8G -----END PGP SIGNATURE-----
