-----BEGIN PGP SIGNED MESSAGE----- Hash: SHA1 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/ iD8DBQFTMqMhUxlJ7aRr7hoRAifWAJ9c9pn4BRy7XcMfgPRzjdw1mJ69vgCgrF9f cnNfRbP5XmA4NdUGxXW4S5A= =HRtQ -----END PGP SIGNATURE-----
