[ccp4bb] Question re: ice rings in diffraction data
Hello all, I have a query re: processing data. I have some lovely diffraction data that has been marred by ice rings (so...not as lovely as it could be). I was told it may be possible to mask the regions of the ice rings (obviously sacrificing completeness) during processing. I have been using HKL2000 to process data. Is this feature available with this program? Otherwise, we also have Mosfilm. Any advice would be greatly appreciated. Thank you. Sincerely in anticipation Mona Rahman --- Mona N. Rahman, Ph.D. Dept. of Biochemistry/Pharmacology Toxicology Botterell Hall, Rooms 623 and 634 (lab) Queen's University, Kingston, ON, K7L 3N6 Phone: 613-533-2993, 613-533-6293 (lab) E-mail: [EMAIL PROTECTED]
Re: [ccp4bb] Question re: ice rings in diffraction data
One can try to set the high resolution to exlude the ice ring ONLY during autoindexing. Once Denzo picks the correct lattice, then you can include the highest resolution available during the refinement. or One can pick fewer peaks during the peak search in hope that the ice ring will be dropped. In this case, if only a few ice ring reflections are picked, one can manually Pick(Remove) reflections also. Good luck, Jeff Quoting Mona Rahman [EMAIL PROTECTED]: Hello all, I have a query re: processing data. I have some lovely diffraction data that has been marred by ice rings (so...not as lovely as it could be). I was told it may be possible to mask the regions of the ice rings (obviously sacrificing completeness) during processing. I have been using HKL2000 to process data. Is this feature available with this program? Otherwise, we also have Mosfilm. Any advice would be greatly appreciated. Thank you. Sincerely in anticipation Mona Rahman --- Mona N. Rahman, Ph.D. Dept. of Biochemistry/Pharmacology Toxicology Botterell Hall, Rooms 623 and 634 (lab) Queen's University, Kingston, ON, K7L 3N6 Phone: 613-533-2993, 613-533-6293 (lab) E-mail: [EMAIL PROTECTED]
Re: [ccp4bb] Question re: ice rings in diffraction data
Dear Mona, If you used XDS to process the data you could use the EXCLUDE_RESOLUTION_RANGE keyword to exactly do what you describe. Best regards, Alexander Mit freundlichen Grüßen / Best regards / Cordialement Alexander Schiffer Sanofi-Aventis Deutschland GmbH RD CAS Structural Biology FFM Industriepark Hoechst Bldg. G877, Room 029 D-65926 Frankfurt am Main f: +49 69 305 24896 f: +49 69 305 80169 w:www.sanofi-aventis.de 125 Jahre Arzneimittel aus Deutschland von sanofi-aventis ** Sanofi-Aventis Deutschland GmbH · Sitz der Gesellschaft: Frankfurt am Main · Handelsregister: Frankfurt am Main, Abt. B Nr. 40661 Vorsitzender des Aufsichtsrats: Hanspeter Spek - Geschäftsführer: Dr. Heinz-Werner Meier (Vorsitzender),Dr. Matthias Braun, Hervé Gisserot, Prof. Dr. Dr. Werner Kramer, Dr. Klaus Menken, Dr. Martin Siewert ** From: CCP4 bulletin board [mailto:[EMAIL PROTECTED] On Behalf Of Mona Rahman Sent: Tuesday, July 15, 2008 4:14 PM To: CCP4BB@JISCMAIL.AC.UK Subject: [ccp4bb] Question re: ice rings in diffraction data Hello all, I have a query re: processing data. I have some lovely diffraction data that has been marred by ice rings (so...not as lovely as it could be). I was told it may be possible to mask the regions of the ice rings (obviously sacrificing completeness) during processing. I have been using HKL2000 to process data. Is this feature available with this program? Otherwise, we also have Mosfilm. Any advice would be greatly appreciated. Thank you. Sincerely in anticipation Mona Rahman --- Mona N. Rahman, Ph.D. Dept. of Biochemistry/Pharmacology Toxicology Botterell Hall, Rooms 623 and 634 (lab) Queen's University, Kingston, ON, K7L 3N6 Phone: 613-533-2993, 613-533-6293 (lab) E-mail: [EMAIL PROTECTED]
Re: [ccp4bb] Question re: ice rings in diffraction data
Look at the reject fraction keyword and increase the value, as described on pp 39-40 of the manual Pete From: CCP4 bulletin board [mailto:[EMAIL PROTECTED] On Behalf Of Mona Rahman Sent: Tuesday, July 15, 2008 7:14 AM To: CCP4BB@JISCMAIL.AC.UK Subject: [ccp4bb] Question re: ice rings in diffraction data Hello all, I have a query re: processing data. I have some lovely diffraction data that has been marred by ice rings (so...not as lovely as it could be). I was told it may be possible to mask the regions of the ice rings (obviously sacrificing completeness) during processing. I have been using HKL2000 to process data. Is this feature available with this program? Otherwise, we also have Mosfilm. Any advice would be greatly appreciated. Thank you. Sincerely in anticipation Mona Rahman --- Mona N. Rahman, Ph.D. Dept. of Biochemistry/Pharmacology Toxicology Botterell Hall, Rooms 623 and 634 (lab) Queen's University, Kingston, ON, K7L 3N6 Phone: 613-533-2993, 613-533-6293 (lab) E-mail: [EMAIL PROTECTED]
Re: [ccp4bb] Question re: ice rings in diffraction data
Hi You can exclude the ice rings easily in Mosflm - from the command line - (a) Autoindexing - AUTOINDEX EXCLUDE ICE (but see user guide for more on this) (b) Processing - RESOLUTION EXCLUDE ICE Or if you try iMosflm, just check the button that says exclude ice rings (Indexing pane) or Do not integrate near ice rings (Processing pane). These are good for hexagonal ice (what you probably have), but if you've got cubic (or other) ice, you need to exclude the rings by their explicit resolution. On 15 Jul 2008, at 15:14, Mona Rahman wrote: Hello all, I have a query re: processing data. I have some lovely diffraction data that has been marred by ice rings (so...not as lovely as it could be). I was told it may be possible to mask the regions of the ice rings (obviously sacrificing completeness) during processing. I have been using HKL2000 to process data. Is this feature available with this program? Otherwise, we also have Mosfilm. Any advice would be greatly appreciated. Thank you. Sincerely in anticipation Mona Rahman --- Mona N. Rahman, Ph.D. Dept. of Biochemistry/Pharmacology Toxicology Botterell Hall, Rooms 623 and 634 (lab) Queen's University, Kingston, ON, K7L 3N6 Phone: 613-533-2993, 613-533-6293 (lab) E-mail: [EMAIL PROTECTED] Harry -- Dr Harry Powell, MRC Laboratory of Molecular Biology, MRC Centre, Hills Road, Cambridge, CB2 2QH
Re: [ccp4bb] Question re: ice rings in diffraction data
Dear Mona, Yes. You can get Denzo to reject reflections on or close to ice rings, or any other features with highly irregular background variations, by increasing the value of the REJECT keyword (see p. 40 of the HKL2000 manual by D. Gerwith, http://www.hkl-xray.com/hkl_web1/hkl/manual_online.pdf). HTH, Joe Hello all, I have a query re: processing data. I have some lovely diffraction data that has been marred by ice rings (so...not as lovely as it could be). I was told it may be possible to mask the regions of the ice rings (obviously sacrificing completeness) during processing. I have been using HKL2000 to process data. Is this feature available with this program? Otherwise, we also have Mosfilm. Any advice would be greatly appreciated. Thank you. Sincerely in anticipation Mona Rahman --- Mona N. Rahman, Ph.D. Dept. of Biochemistry/Pharmacology Toxicology Botterell Hall, Rooms 623 and 634 (lab) Queen's University, Kingston, ON, K7L 3N6 Phone: 613-533-2993, 613-533-6293 (lab) E-mail: [EMAIL PROTECTED]
