> In fact, just estimating ORGX and ORGY from the first frame, using adxv or > > XDS-viewer, seems to do a good job.
The silver lining of having ice (or any other kind) rings is that one can determine the origin rather accurately by just finding the center of these rings. Cheers, N. Ruslan Sanishvili (Nukri), Ph.D. GM/CA-CAT Biosciences Division, ANL 9700 S. Cass Ave. Argonne, IL 60439 Tel: (630)252-0665 Fax: (630)252-0667 rsanishv...@anl.gov -----Original Message----- From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Kay Diederichs Sent: Saturday, October 15, 2011 6:10 AM To: CCP4BB@JISCMAIL.AC.UK Subject: Re: [ccp4bb] data processing problem with ice rings Hi ChenTiantian, the R-factors and I/sigma are bad even at low resolution where the first icering does not influence the results. Thus, the problem with your data processing has little to do with the icerings. I guess that the indexing is not correct. My suggestion: 1) using adxv or a similar display program, note what the inner and outer limits of the ice rings are. These values should be used as parameters for the EXCLUDE_RESOLUTION_RANGE= keywords in XDS.INP, not the provided ones (which are meant for hexagonal ice). 2) start XDS from the INIT step 3) use at least half of your DATA_RANGE as SPOT_RANGE 4) make sure that ORGX and ORGY are correct - mis-indexing is in 90% of the cases due to a wrong origin. In fact, just estimating ORGX and ORGY from the first frame, using adxv or XDS-viewer, seems to do a good job. HTH, Kay Am 20:59, schrieb ChenTiantian: > Hi there, > I am processing a dataset which has bad ice rings (as you can see in the > attach png file). > I tried both XDS and imosflm, and got similar results, it seems that > adding " EXCLUDE_RESOLUTION_RANGE" cannot get rid of the effects of the > ice rings. > the following is part of the CORRECT.LP which is the second attached > file, you can find more details there. > > SUBSET OF INTENSITY DATA WITH SIGNAL/NOISE >= -3.0 AS FUNCTION OF > RESOLUTION > RESOLUTION NUMBER OF REFLECTIONS COMPLETENESS R-FACTOR > R-FACTOR COMPARED I/SIGMA R-meas Rmrgd-F Anomal SigAno Nano > LIMIT OBSERVED UNIQUE POSSIBLE OF DATA observed > expected Corr > > 4.24 37152 5537 5545 99.9% 46.9% > 52.7% 37150 2.48 50.8% 19.4% -28% 0.513 5136 > 3.01 55344 9002 9840 91.5% 62.7% > 65.1% 55116 1.76 68.3% 48.1% -28% 0.520 7760 > 2.46 84636 12699 12703 100.0% 67.4% > 84.7% 84634 1.55 73.0% 54.2% -19% 0.513 12104 > 2.13 97910 14743 14987 98.4% 254.5% > 199.3% 97908 0.16 276.2% 4899.9% -23% 0.473 14037 > 1.90 110260 16846 16940 99.4% 299.2% > 303.3% 110245 0.06 325.0% -99.9% -17% 0.422 15995 > 1.74 118354 18629 18744 99.4% 1062.0% > 1043.6% 118317 -0.20 1156.4% -99.9% -13% 0.380 17414 > 1.61 122958 20193 20331 99.3% 967.5% > 1571.1% 122868 0.10 1059.7% 987.3% -2% 0.402 18348 > 1.51 125075 21554 21794 98.9% 838.9% > 1355.1% 124933 0.08 922.6% 1116.9% -1% 0.402 18977 > 1.42 72057 17042 23233 73.4% 640.8% > 775.3% 70391 0.08 732.5% 826.7% -8% 0.425 10003 > total 823746 136245 144117 94.5% 166.4% > 166.7% 821562 0.40 181.1% 296.7% -15% 0.435 119774 > > Note that I/SIGMA of each resolution shell is <2.5, so how should I do > to process the dataset properly? Any suggestion about this super ice rings? > Thanks! > > Tiantian > > -- > Shanghai Institute of Materia Medica, Chinese Academy of Sciences > Address: Room 101, 646 Songtao Road, Zhangjiang Hi-Tech Park, > Shanghai, 201203 -- Kay Diederichs http://strucbio.biologie.uni-konstanz.de email: kay.diederi...@uni-konstanz.de Tel +49 7531 88 4049 Fax 3183 Fachbereich Biologie, Universität Konstanz, Box 647, D-78457 Konstanz This e-mail is digitally signed. If your e-mail client does not have the necessary capabilities, just ignore the attached signature "smime.p7s".
