Kate, under linux environment my pdb_extract_sf from the CCP4 installation doesn’t work from command line due to the next error:
Error, can not get file(data_template.cif). Please set PDB_EXTRACT environment I had created PDB_EXTRACT and pointed it to CCP4 home folder (actual sh command in bold): $*PDB_EXTRACT=”$CCP4”; export PDB_EXTRACT* After that pdb_extract works well: $*pdb_extract_sf -idat gbnirno2.mtz -o refine.cif* *Converting gbnirno2.mtz to the mmCIF format...* *Warning: No wavelength value was found in SF file. A dot is added to cif token.* *The output file name: refine.cif* Refine.cif now contains _refln.status. I guess this column for free reflections contain “f” mark. Am I right? ср, 22 авг. 2018 г. в 0:28, Kate Hoffmann <khoffm...@callutheran.edu>: > Hello list, > > I've been trying to deposit several structures using CCP4 7.0.061 and > finding an error with PDB_extract that I can't seem to overcome. > Specifically, the generated reflection.cif file doesn't include the freeR > set (confirmed with the deposition program at RCSB and by visual inspection > of the file). I have successfully been using an assigned freeR set in > refmac and PDB_redo/validation, but I can't seem to get it attached in > mmCIF. Has anyone run into this and solved it? Should I be preparing files > from a different subfolder or job? I have updated CCP4 and also tried > running PDB_extract on the webserver, but no luck. Your guidance is most > welcome. > > Thanks in advance. > > -Kate > > Katherine M. Hoffmann, Ph.D. > John L. Stauffer Professor of Analytical Chemistry > California Lutheran University > 60 West Olsen Road, #3700 > Thousand Oaks, CA 91360 > 805-493-3916 > > ######################################################################## > > To unsubscribe from the CCP4BB list, click the following link: > https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB&A=1 > -- Eugene Osipov Junior Research Scientist Laboratory of Enzyme Engineering Research Center of Biotechnology Russian Academy of Sciences Leninsky pr. 33, 119071 Moscow, Russia e-mail: e.m.osi...@gmail.com ######################################################################## To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB&A=1
