2008/7/2
Adding to my previous post, I have found another strange issue (possibly a bug?) concerning special positions: In my case, the "special" atom (a cation on a three-fold in sg I23), while being considered during refinement, seems to be completely omitted (or heavily downweighted) for map calculations! The 2fo-fc map shows a "hole" at this position, while there is huge difference density in the fo-fc map (largely irrespective of whether or not the occupancy is reduced in the input.) The same pdb file, used in cns just for map calculation, gives a beautiful density at the cation position, while the rest of the map is more or less identical.
Hi Oliver, I don't have any links to manual or anything of that sort, but I refined a metal ion on a 2-fold axis and I simply put the atom exactly on the special position. That seemed to work just fine... Hope this helps, Folmer
At the moment I cannot think of any error in the input since refinement of the atom does take place, with the proper restrictions due to the three-fold axis. But something is going seriously wrong.
Any ideas? Oliver
------------------------------- Dr. Oliver H. Weiergraeber Institute of Neurosciences and Biophysics Molecular Biophysics Research Centre Juelich D-52425 Juelich Germany Phone: +49-2461-612028 Fax: +49-2461-612020 -------------------------------
----- Original Message ----- From: [email protected] Date: Wednesday, July 2, 2008 2:55 pm Subject: [phenixbb] special positions
Hello,
a very simple question (although I could not find *anything* about this in the documentation!): What does phenix.refine expect as occupancy for an atom on a special position: reduced occupancy (like refmac) or full occupancy (like cns_solve)?
Oliver
------------------------------- Dr. Oliver H. Weiergraeber Institute of Neurosciences and Biophysics Molecular Biophysics Research Centre Juelich D-52425 Juelich Germany Phone: +49-2461-612028 Fax: +49-2461-612020 -------------------------------
------------------------------------------------------------------- ------------------------------------------------------------------- Forschungszentrum Juelich GmbH 52425 Juelich
Sitz der Gesellschaft: Juelich Eingetragen im Handelsregister des Amtsgerichts Dueren Nr. HR B 3498 Vorsitzende des Aufsichtsrats: MinDir'in Baerbel Brumme-Bothe Geschaeftsfuehrung: Prof. Dr. Achim Bachem (Vorsitzender), Dr. Ulrich Krafft (stellv. Vorsitzender), Prof. Dr. Harald Bolt, Dr. Sebastian M. Schmidt ------------------------------------------------------------------- ------------------------------------------------------------------- _______________________________________________ phenixbb mailing list [email protected] http://www.phenix-online.org/mailman/listinfo/phenixbb
------------------------------------------------------------------- ------------------------------------------------------------------- Forschungszentrum Juelich GmbH 52425 Juelich
Sitz der Gesellschaft: Juelich Eingetragen im Handelsregister des Amtsgerichts Dueren Nr. HR B 3498 Vorsitzende des Aufsichtsrats: MinDir'in Baerbel Brumme-Bothe Geschaeftsfuehrung: Prof. Dr. Achim Bachem (Vorsitzender), Dr. Ulrich Krafft (stellv. Vorsitzender), Prof. Dr. Harald Bolt, Dr. Sebastian M. Schmidt ------------------------------------------------------------------- ------------------------------------------------------------------- _______________________________________________ phenixbb mailing list [email protected] http://www.phenix-online.org/mailman/listinfo/phenixbb