Dear Gyuhyeok, Please feel free to describe any challenges with settings for Careless at https://github.com/rs-station/careless/issues We will be happy to help and improve our online documentation accordingly.
I assume some of the statistics you report below are simply duplicated from Aimless? We did not implement calculations for R-merge, R-meas, and R-pim. Careless can currently report CC1/2, CCanom (if Friedel mates were kept apart), Rsplit, and a new quantity, CCpred, based on prediction of expected intensities for a heldout test set of integrated intensities. To do so, make sure you use the “--merge-half-datasets” and “--half-dataset-repeats N” (with N some number of repeats) when running Careless. You can then use “careless.cchalf your_output_xval.mtz” to obtain CC1/2. There are some curious differences between your refinements (for example, 203 versus 13 solvent molecules) that may or may not be directly related to Careless. If you are willing to share your PDB and MTZ files, we’d be very interested. Thanks, Doeke From: CCP4 bulletin board <CCP4BB@JISCMAIL.AC.UK> On Behalf Of "???" Sent: Sunday, January 8, 2023 9:45 PM To: CCP4BB@JISCMAIL.AC.UK Subject: Re: [ccp4bb] Careless and negative Wilson B-factor Dear Eleanor, I agree that the decrease in the B-factor is likely due to "Careless." The author of this article seems to recognize Wilson B-factor issues during the peer review process (https://static-content.springer.com/esm/art%3A10.1038%2Fs41467-022-35280-8/MediaObjects/41467_2022_35280_MOESM2_ESM.pdf) and offers some options for addressing them (such as the --wilson-prior-b WILSON_PRIOR_B option). It may take some time for me to get the software running correctly. Gyuhyeok P.S. I have attached some preliminary statistics using datasets from Careless or Aimless. Please note that both the Atomic B-factor and the Wilson B-factor are significantly reduced in Careless data. Merging tool Carelss Aimless Wavelength 1.0000 1.0000 Resolution range 37.98 - 2.60 (2.69 - 2.60) 43.06 - 2.60 (2.69 - 2.60) Space group I 2 3 I 2 3 Unit cell 161.128 161.128 161.128 90 90 90 161.128 161.128 161.128 90 90 90 Total reflections 886846 (79364) 886852 (79364) Unique reflections 21520 (2135) 21522 (2135) Multiplicity 41.2 (37.2) 41.2 (37.2) Completeness (%) 99.95 (100.00) 99.94 (99.95) Mean I/sigma(I) 14.2 (0.8) 14.2 (0.8) Wilson B-factor -0.91 74.5 R-merge 0.240 (4.566) 0.240 (4.566) R-meas 0.243 (4.629) 0.243 (4.629) R-pim 0.038 (0.757) 0.038 (0.757) CC1/2 0.998 (0.362) 0.997 (0.362) CC* 0.999 (0.729) 0.999 (0.729) Reflections used in refinement 21520 (2135) 21519 (2134) Reflections used for R-free 1118 (112) 1118 (112) R-work 0.2027 (0.2547) 0.2093 (0.3422) R-free 0.2601 (0.3282) 0.2564 (0.3634) CC(work) 0.664 (0.708) 0.919 (0.622) CC(free) 0.622 (0.569) 0.766 (0.478) Number of non-hydrogen atoms 3930 3740 macromolecules 3655 3655 ligands 72 72 solvent 203 13 Protein residues 443 443 RMS(bonds) 0.008 0.009 RMS(angles) 1.030 1.110 Ramachandran favored (%) 95.4 93.2 Ramachandran allowed (%) 4.3 6.4 Ramachandran outliers (%) 0.2 0.5 Rotamer outliers (%) 2.0 3.3 Clashscore 8.95 8.41 Average B-factor 19.9 70.2 macromolecules 19.7 70.0 ligands 31.1 81.5 solvent 20.1 61.5 body,div,table,thead,tbody,tfoot,tr,th,td,p { font-family:"Liberation Sans"; font-size:x-small }a.comment-indicator:hover + comment { background:#ffd; position:absolute; display:block; border:1px solid black; padding:0.5em; }a.comment-indicator { background:red; display:inline-block; border:1px solid black; width:0.5em; height:0.5em; }comment { display:none; } --------- 원본 메일 --------- 보낸사람 : Eleanor Dodson <eleanor.dod...@york.ac.uk<mailto:eleanor.dod...@york.ac.uk>> 받는사람 : <gyuhyeok...@gist.ac.kr<mailto:gyuhyeok...@gist.ac.kr>> 받은날짜 : 2023/Jan/8(Sun) 10:39:39 제목 : Re: [ccp4bb] Careless and negative Wilson B-factor I suppose so, but I would refine your final model against the initial data too, and see what R factors you get.. Eleanor On Fri, 6 Jan 2023 at 14:46, "조규혁" <gyuhyeok...@gist.ac.kr<mailto:gyuhyeok...@gist.ac.kr>> wrote: Dear Eleanor, I was wondering if the model and structure factors with the negative Wilson B-factor can be deposited in the PDB or made interpretable for biochemical experiments. The data were initially processed in XDS and the CORRECT output (XDS_ASCII.HKL) was provided to Careless. Sincerely, Gyuhyeok --------- 원본 메일 --------- 보낸사람 : Eleanor Dodson <eleanor.dod...@york.ac.uk<mailto:eleanor.dod...@york.ac.uk>> 받는사람 : <gyuhyeok...@gist.ac.kr<mailto:gyuhyeok...@gist.ac.kr>> 참조 : <CCP4BB@jiscmail.ac.uk<mailto:CCP4BB@jiscmail.ac.uk>> 받은날짜 : 2023/Jan/6(Fri) 20:09:57 제목 : Re: [ccp4bb] Careless and negative Wilson B-factor 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<mailto: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<https://urldefense.proofpoint.com/v2/url?u=https-3A__github.com_rs-2Dstation_careless&d=DwMGaQ&c=WO-RGvefibhHBZq3fL85hQ&r=DPfbtiuJFZDsaMqRC3wABRuP0iJZMKOIsdAAHocfxcg&m=G8ola-jC0CPvLE0DV2wZ49cLeryph82jWMF7PWb1OigxNHkm6iyH2nNXIqExASJr&s=ZToh8wmWIXVLX5j1p0ydDZ94lNBnXbmq7L1iqKHPdaw&e=>). 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<mailto:gyuhyeok...@gist.ac.kr> [https://gist.ac.kr:443/resources/theme/default/images/sign/mail_banner_2019.jpg] ________________________________ To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1<https://urldefense.proofpoint.com/v2/url?u=https-3A__www.jiscmail.ac.uk_cgi-2Dbin_WA-2DJISC.exe-3FSUBED1-3DCCP4BB-26A-3D1&d=DwMGaQ&c=WO-RGvefibhHBZq3fL85hQ&r=DPfbtiuJFZDsaMqRC3wABRuP0iJZMKOIsdAAHocfxcg&m=G8ola-jC0CPvLE0DV2wZ49cLeryph82jWMF7PWb1OigxNHkm6iyH2nNXIqExASJr&s=ks9DcDFK2GsatlGOtElA8IaoX6q2GfNxwZHsGu3axjY&e=> 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<mailto:gyuhyeok...@gist.ac.kr> [https://gist.ac.kr:443/resources/theme/default/images/sign/mail_banner_2019.jpg] ________________________________ To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1<https://urldefense.proofpoint.com/v2/url?u=https-3A__www.jiscmail.ac.uk_cgi-2Dbin_WA-2DJISC.exe-3FSUBED1-3DCCP4BB-26A-3D1&d=DwMGaQ&c=WO-RGvefibhHBZq3fL85hQ&r=DPfbtiuJFZDsaMqRC3wABRuP0iJZMKOIsdAAHocfxcg&m=G8ola-jC0CPvLE0DV2wZ49cLeryph82jWMF7PWb1OigxNHkm6iyH2nNXIqExASJr&s=ks9DcDFK2GsatlGOtElA8IaoX6q2GfNxwZHsGu3axjY&e=> 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<mailto:gyuhyeok...@gist.ac.kr> [https://gist.ac.kr:443/resources/theme/default/images/sign/mail_banner_2019.jpg] ________________________________ To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1<https://urldefense.proofpoint.com/v2/url?u=https-3A__www.jiscmail.ac.uk_cgi-2Dbin_WA-2DJISC.exe-3FSUBED1-3DCCP4BB-26A-3D1&d=DwMGaQ&c=WO-RGvefibhHBZq3fL85hQ&r=DPfbtiuJFZDsaMqRC3wABRuP0iJZMKOIsdAAHocfxcg&m=G8ola-jC0CPvLE0DV2wZ49cLeryph82jWMF7PWb1OigxNHkm6iyH2nNXIqExASJr&s=ks9DcDFK2GsatlGOtElA8IaoX6q2GfNxwZHsGu3axjY&e=> ######################################################################## 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/
