Hi Gyuhyeok and everyone, Thank you. We developed Careless to support scaling and merging of data from a wide range of diffraction experiments, including Laue, XFEL, time-resolved/serial, etc. Nice to hear that your electron density maps look promising. This is new software and we will continue to learn from all user feedback!
In Careless, the observations are scaled using the assumption that overall the amplitudes of the corresponding structure factors follow the Wilson distribution (see, for example, https://www-structmed.cimr.cam.ac.uk/Course/Statistics/statistics.html). By default, this means that the average structure factor amplitude does not fall off with resolution (a global B = 0). In this sense, the Careless output is normalized, as Kay observed. (there is a subtle difference with 'official' normalized structure factors, as described, for example, in section 7.10 of Rupp's textbook, Biomolecular Crystallography). Real data, of course, show a decrease in diffraction intensity with resolution-something that usually gets worse with radiation dose. Scaling algorithms attempt to correct integrated intensities to all follow the same scaling behavior, for example matching the first frame. In Careless, you can specify an expected overall B factor by adding a flag, for example --wilson-prior-b 17.0 specifies the expectation of an overall B factor of 17 A^2, rather than 0. It should make Xtriage's error go away. So far, we have found that the default typically works just fine for molecular replacement and structure refinement. We have also successfully used Careless output for phasing with SHELX* and Phaser. The PDB is aware of Careless and you can specify it as the scaling program used. Please let us know if you encounter any difficulties with deposition. As a reminder, Careless is free, open-source software. We encourage everyone to file "issues", including bugs and feature requests, on the GitHub repo. If you'd like to extend the capabilities of Careless for your own purposes, you can do so yourself too! Code & Installation instructions: https://github.com/rs-station/careless Usage examples: https://github.com/rs-station/careless-examples Publication: https://www.nature.com/articles/s41467-022-35280-8 -- Doeke 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: [log in to unmask]<https://www.jiscmail.ac.uk/cgi-bin/wa-jisc.exe?LOGON=A3%3Dind2301%26L%3DCCP4BB%26E%3Dbase64%26P%3D6895021%26B%3D---%253DPart.a316.e6cfa70efc5cf13a.1858627e0e0.e78daba8b74bda93%253D-%26T%3Dtext%252Fhtml%3B%2520charset%3DUTF-8%26pending%3D> [cid:image002.jpg@01D92396.2A1F4820] ________________________________ 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/
