Hi Florian, I have found that, in some cases, playing with -ncs-mask-filter-radius can help parrot to successfully detect and apply ncs averaging. In one recent case, with 8 molecules where NCS was not found without this option, values from 14 to 30 angstroms worked (but gave maps of variable quality). I don't know what's the default value for this.
Best regards, Pierre Legrand, PROXIMA-1 Phone-office +33 1 69 35 96 60 Phone-beamline +33 1 69 35 97 38 http://www.synchrotron-soleil.fr/Recherche/LignesLumiere/PROXIMA1 -----Original Message----- From: CCP4 bulletin board on behalf of Florian Schmitzberger Sent: Fri 9/3/2010 9:34 PM To: CCP4BB@JISCMAIL.AC.UK Subject: [ccp4bb] Problem with NCS detection in Parrot Dear All, I am encountering a problem when using Parrot (for combined density modification and non crystallographic symmetry (NCS) averaging) in ccp4 6.1.13, run via ccp4i. Parrot does not detect the (2-fold) NCS present among my heavy atom substructure with 20 seleniums (the pdb was output by Phaser-EP, single chain ID, and is read by Parrot from what I can tell). I have tried a to split the NCS related heavy atoms into separate chains, but Parrot does still not appear to detect any NCS (error message: WARNING: No NCS found from heavy atoms). The Professs program seems to detect the NCS readily. Unfortunately, I don't think it is possible to input externally determined NCS operators into Parrot. Regards, Florian ----------------------------------------------------------- Florian Schmitzberger Biological Chemistry and Molecular Pharmacology Harvard Medical School 250 Longwood Avenue, SGM 130 Boston, MA 02115, US Tel: 001 617 432 5602
