Hi, As of last week, this is a "known bug" (defined as one where I got around to adding it to the list on our Phaser Wiki). It has been fixed in the latest nightly builds of Phenix, and a new executable will be released through CCP4 in a few weeks, coordinated with the next stable release of Phenix.
It only happens under very specific circumstances, i.e. when you say "SGALTERNATIVE SELECT LIST" and then give a list with only one element. We didn't think this would happen much because we thought that, if people know which space group they should be using, they will put the correct space group in the MTZ file. If you don't know the correct space group, it's pretty easy to list all of the possibilities in one job and then you don't run into this bug. The new version of Phaser is more clever than the old one about choosing the correct space group (it used to make such decisions prematurely, but now waits until the choice is unambiguous), so there shouldn't be a real incentive to submitting separate jobs for the possible space groups. Thanks for reporting it, and sorry for the trouble! Randy Read On 20 Aug 2012, at 16:06, Jan Abendroth wrote: > Hi all, > we have been running into a space group issue when we start phaser (2.5.1) > through ccp4i since the installation of ccp4-6.3.0: > > We typically scale data in the point group and then let Phaser go through > various space groups. Even though the corresponding line appears in the input > file > SGALTERNATIVE SELECT LIST > SGALTERNATIVE TEST P41 > rotation and translation function would only run in the space group provided > by the mtz file. Obviously it does not matter for the rotation function. > > As a work around one can edit the input file (run& view com file), by > replacing the two lines mentioned above with > SPACEGROUP P41 > This is a bit inconvenient though. > > Any ideas what is going wrong with the standard way? > > Cheers, > Jan > -- > Jan Abendroth > Emerald BioStructures > Seattle / Bainbridge Island WA, USA > home: Jan.Abendroth_at_gmail.com > work: JAbendroth_at_embios.com > http://www.emeraldbiostructures.com ------ Randy J. Read Department of Haematology, University of Cambridge Cambridge Institute for Medical Research Tel: + 44 1223 336500 Wellcome Trust/MRC Building Fax: + 44 1223 336827 Hills Road E-mail: rj...@cam.ac.uk Cambridge CB2 0XY, U.K. www-structmed.cimr.cam.ac.uk
