Thank you for your help, I had the write rejection file set to 0.5 and probability at 0.001. It seems that I had so many rejections that it was hard to get rid of all of them. I have obtained a script to keep running scalepack until all of the rejections are gone from the log file. It takes a very long time to run but it is better than hitting enter over and over.
Although I have read the manual I am still having some difficulty understanding the difference between rejection file and the probability. If rejection file is set to 0.5 I'm guessing that if a reflection has a 50% probability of being an outlier it will be written to the log file. But I don't understand how the rejection probability interplays here. Thanks for any help you can provide. -Yarrow > Yarrow, > > as far as I know, scalepack, scalepackvirus and the other variants only > differ by their respective array sizes (Someone from Wladek's or ZO's > lab may be more suitable to comment on this). The rejections in the log > file are controlled by the parameters 'write rejection file xxx' and > 'rejection probability'. You may want to read up on those in the manual. > I believe that historically the way it was supposed to work is that > rejection candidates are written to the log file for examination and > then in subsequent rounds are written to the 'reject' file. The latter > is determined by the 'write rejection file' parameter. > > No, scalepack does not output the rmeas or rpim values. I have some > recollection that Manfred Weiss at EMBL wrote a program which could > analyze scalepack data written with 'no merge original index' to yield > those parameters, you may want to look into this. The name of the > fortran source is 'rmerge.f'. Unfortunately the link to the original > source repository is dead, but I have a copy around, which I could > share. > > Another way would be to go the route of scalepack unmerged data -> > pointless -> scala, although I have never tried that myself. > > Good luck > > Carsten > > > -----Original Message----- > From: CCP4 bulletin board [mailto:[email protected]] On Behalf Of > Yarrow Madrona > Sent: Tuesday, December 06, 2011 11:04 AM > To: [email protected] > Subject: [ccp4bb] scalepackvirus rejections and Rrin > > Hello, > > I am using scalepackvirus and I noticed that the rejection list grows > but > does not disappear in later rounds of scaling from the log file as in > scalepack. I am assuming that the rejections are treated the same way as > in scalepack but for some reason are not removed from the log file. > Does > anyone know if this is correct? > > Also I wondered if there is any way to get a redundancy dependent R > value > from scalepack. Thank you. > > -Yarrow > > -- > Yarrow Madrona > > Graduate Student > Molecular Biology and Biochemistry Dept. > University of California, Irvine > Natural Sciences I, Rm 2403 > Irvine, CA 92697 > > > -- Yarrow Madrona Graduate Student Molecular Biology and Biochemistry Dept. University of California, Irvine Natural Sciences I, Rm 2403 Irvine, CA 92697
