The tool must have sharpened your data - sometimes enhancing the outer data does improve the electron density.. So I wouldnt worry about that "negative" B factor - it is doubtless a result of the "careless" run, and not presumably the one you got at the data processing step.. Eleanor
On Fri, 6 Jan 2023 at 08:27, "조규혁" <gyuhyeok...@gist.ac.kr> wrote: > Dear all, > > I recently tested a novel merging tool for crystallography data called > Careless (https://github.com/rs-station/careless). > > When I used it on our 2.6 A-resolution structure in the I23 space group > with a lipid bound structure, I noticed that the electron density > surrounding the acyl chain was significantly improved. > > However, I am concerned about the Wilson B-factor. The Phenix.table_one > tool reports that the Wilson B-factor of the merged mtz file is -0.91. > Phenix.Xtriage warns that a negative Wilson B-factor can be an indication > of unusual pathology or artificial manipulation. > > Has anyone else encountered similar conditions? Are there any > circumstances in which a negative Wilson B-factor can be rationalized? > > Thank you, > Gyuhyeok > > > P.S. Here is the part of the output of Phenix.table_one. > > > Wavelength 1.0000 > Resolution range 37.98 - 2.60 > (2.69 - 2.60) > Space group I 2 3 > Unit cell 161.128 161.128 161.128 > 90 90 90 > Total reflections 886846 (79364) > Unique reflections 21520 (2135) > Multiplicity 41.2 (37.2) > Completeness (%) 99.95 (100.00) > Mean I/sigma(I) > > 14.2 (0.8) > * Wilson B-factor* *-0.91* > R-merge 0.240 (4.566) > R-meas 0.243 (4.629) > R-pim 0.038 (0.757) > CC1/2 0.998 (0.362) > CC* 0.999 (0.729) > > > > > > PhD student > > Department of Chemistry > > Gwangju Institute of Science and Technology (GIST) > 123 Cheomdangwagi-ro, Buk-gu, Gwangju, 61005 > > Republic of Korea > > Tel. +82 62-715-4633 > > e-mail: gyuhyeok...@gist.ac.kr > > > > > ------------------------------ > > To unsubscribe from the CCP4BB list, click the following link: > https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1 > ######################################################################## To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1 This message was issued to members of www.jiscmail.ac.uk/CCP4BB, a mailing list hosted by www.jiscmail.ac.uk, terms & conditions are available at https://www.jiscmail.ac.uk/policyandsecurity/
