Hi Nick, that is certainly not normal, this first step may take minutes (or tens of seconds with small datasets) to run and the logfile is continuously updated. From your report it seems that from some reason it got stuck right at the beginning of your job. I have not seen this issue before. Can you try to kill that job without removing it and send me the log file (or the last ~50 lines with the error message) from it? That should tell us where it got stuck.
Indeed, sometimes it happens that the MR phases and the SAD phases are inconsistent / difficult to combine and a better solution can be achieved by running SAD only (only using the MR model heavy atoms). It differs from case to case. It is usually a good idea to try both approaches if possible. Greetings, Pavol >> From: Nick Huang <huangn...@gmail.com> >> Date: Sat, Jan 31, 2015 at 5:46 PM >> Subject: [ccp4bb] How long does it take crank 2 (refmac step) to run? >> To: CCP4BB@jiscmail.ac.uk >> >> >> Hi all, >> I started a crank 2 process to run a SAD model building with a partial >> model input yesterday. From the log file, crank 2 was in the step of >> "Starting >> process of iterative refinement and (substructure) atom picking" and had >> been running a whole night without any further output. Does anybody know if >> it is normal or there is an error? >> Thanks, >> Nick Huang >> >> Hauptman-Woodward Institute >> >> >> > -- Pavol Skubak Biophysical Structural Chemistry Gorleaus Laboratories Einsteinweg 55 Leiden University LEIDEN 2333CC the Netherlands tel: 0031715274414 web: http://bsc.lic.leidenuniv.nl/people/skubak-0
