[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
Re: [ccp4bb] scalepackvirus rejections and Rrin
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:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Yarrow Madrona Sent: Tuesday, December 06, 2011 11:04 AM To: CCP4BB@JISCMAIL.AC.UK 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
Re: [ccp4bb] scalepackvirus rejections and Rrin
Folks may wish to watch a webinar I gave on using HKL3000. In the webinar I describe how to calculate an Rmeas from scalepack output and also discuss a few other how-to operations. See www.rigaku.com/protein/webinars-past.html for more viewing pleasure. Jim From: CCP4 bulletin board [CCP4BB@JISCMAIL.AC.UK] on behalf of Yarrow Madrona [amadr...@uci.edu] Sent: Tuesday, December 06, 2011 10:03 AM To: CCP4BB@JISCMAIL.AC.UK 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
Re: [ccp4bb] scalepackvirus rejections and Rrin
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:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Yarrow Madrona Sent: Tuesday, December 06, 2011 11:04 AM To: CCP4BB@JISCMAIL.AC.UK 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
