Dear Diana and CCP4BB subscribers, I apologize for the mess created by our recent communication with Diana. The misunderstanding occurred because my replies to “ALL” went to senders, but were not posted at the CCP4BB site. This happened because my email address changed recently. As a result, Diana could only see my message with comments inserted by Ethan, which was hard to understand.
In reality, I agree with Diana that the riding hydrogens could not be omitted from the PDB submission if they were used during the refinement. This would create questions to the submitted structure because the Depositor refinement statistics would differ from that calculated from the submitted structure missing the hydrogens. Regards, Alex From: Diana Tomchick <diana.tomch...@utsouthwestern.edu> Date: Friday, February 28, 2020 at 12:34 PM To: Alexander Aleshin <aales...@sbpdiscovery.org> Cc: CCP4 <CCP4BB@JISCMAIL.AC.UK> Subject: Re: [ccp4bb] Hydrogens in PDB File [EXTERNAL EMAIL] My structure contains riding hydrogens because (surprise!) the protein contains hydrogens, no matter the resolution of the data. Hydrogens should contribute to the calculated structure factors, because they do contribute to the observed structure factors. If I delete the hydrogens from the coordinates and re-refine the model (even keeping the B-factors constant), the geometry will be worse. When using Refmac, you can opt to explicitly write out the riding hydrogen atoms to the final mmCIF file, why don’t you try that and see if it works for you? From the Phenix documentation web site (https://www.phenix-online.org/documentation/reference/refine_gui.html<https://nam03.safelinks.protection.outlook.com/?url=https%3A%2F%2Fwww.phenix-online.org%2Fdocumentation%2Freference%2Frefine_gui.html&data=02%7C01%7Caaleshin%40sbpdiscovery.org%7Ce21f5ba4e0ee48a2b87908d7bc8da049%7C0b162723004547deb0699f1a7aa955a1%7C0%7C0%7C637185188782353919&sdata=BA18fGAO7IUmBOvQDqI5ZXOpHfIztfyUXBn1EQJP%2FwY%3D&reserved=0>) Optimization methods and other options<https://nam03.safelinks.protection.outlook.com/?url=https%3A%2F%2Fwww.phenix-online.org%2Fdocumentation%2Freference%2Frefine_gui.html%23id9&data=02%7C01%7Caaleshin%40sbpdiscovery.org%7Ce21f5ba4e0ee48a2b87908d7bc8da049%7C0b162723004547deb0699f1a7aa955a1%7C0%7C0%7C637185188782363912&sdata=80mJPVgw5B%2FX%2BU56HczRIq%2Ftb3FtxQ8WB7tcKNGy9MI%3D&reserved=0> Several other options are available for the types of optimization used; these typically apply globally, except as noted. * Automatically add hydrogens to model runs phenix.ready_set to add hydrogen atoms (or deuteriums, if performing neutron crystallography) where appropriate. This usually only affects the R-factors at high resolution, but can be very helpful for improving geometry at any resolution. We recommend using explicit hydrogens on protein, nucleic acid, and ligand molecules throughout refinement. (We do not reocmmend adding hydrogens to waters unless you have exceptionally high resolution.) Hydrogen atoms will still be defined using the "riding" model unless otherwise requested, so they do not add parameters during refinement. (Note that this option can be left on if you already have hydrogen atoms in place and are refining as "riding"; if you are refining against neutron data and/or allowing hydrogen atoms to refine individually, you should uncheck the box, as it will otherwise replace the existing atoms.) Diana ************************************************** Diana R. Tomchick Professor Departments of Biophysics and Biochemistry UT Southwestern Medical Center 5323 Harry Hines Blvd. Rm. ND10.214A Dallas, TX 75390-8816 diana.tomch...@utsouthwestern.edu<mailto:diana.tomch...@utsouthwestern.edu> (214) 645-6383 (phone) (214) 645-6353 (fax) On Feb 28, 2020, at 2:23 PM, Alexander Aleshin <aales...@sbpdiscovery.org<mailto:aales...@sbpdiscovery.org>> wrote: EXTERNAL MAIL Diana, Your structure 6PWD contains riding hydrogens even though the resolution is only 2.5A. So, the lack of differences between Depositor and DCC values does not contradict my point. Now, try to delete the hydrogens and recalculate R/Rfree without re-refining B-factors. You’ll see a noticeable difference. It is because hydrogens contribute to calculated structural factors. Alex From: CCP4 bulletin board <CCP4BB@JISCMAIL.AC.UK<mailto:CCP4BB@JISCMAIL.AC.UK>> on behalf of Diana Tomchick <diana.tomch...@utsouthwestern.edu<mailto:diana.tomch...@utsouthwestern.edu>> Reply-To: Diana Tomchick <diana.tomch...@utsouthwestern.edu<mailto:diana.tomch...@utsouthwestern.edu>> Date: Friday, February 28, 2020 at 11:52 AM To: "CCP4BB@JISCMAIL.AC.UK<mailto:CCP4BB@JISCMAIL.AC.UK>" <CCP4BB@JISCMAIL.AC.UK<mailto:CCP4BB@JISCMAIL.AC.UK>> Subject: Re: [ccp4bb] Hydrogens in PDB File [EXTERNAL EMAIL] Here is just one of many examples that illustrates what I was trying to say about deposition of the final mmCIF file from the final output of Phenix refinement. This is from the freely downloadable PDB validation report for PDB ID 6PWD. Search the PDB on my last name and download several of the validation reports, and if you find one that diverges a lot between the Depositor and DCC values, let me know. They should be so close to the same as to be meaningless, at least for depositions within the last 3-5 years (older ones may indeed diverge a lot, but we all can’t be held responsible for the outputs of now-obsolete software). Diana ________________________________ UT Southwestern Medical Center The future of medicine, today. ________________________________ To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB&A=1<https://nam03.safelinks.protection.outlook.com/?url=https%3A%2F%2Fwww.jiscmail.ac.uk%2Fcgi-bin%2Fwebadmin%3FSUBED1%3DCCP4BB%26A%3D1&data=02%7C01%7Caaleshin%40sbpdiscovery.org%7Ce21f5ba4e0ee48a2b87908d7bc8da049%7C0b162723004547deb0699f1a7aa955a1%7C0%7C0%7C637185188782363912&sdata=Rwvu9Yyhl2AHtXsc4kUQKR%2FhWA9kDTOhoRAJQYiwFCk%3D&reserved=0> CAUTION: This email originated from outside UTSW. 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