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Send phenixbb mailing list submissions to [email protected] To subscribe or unsubscribe via email, send a message with subject or body 'help' to [email protected] You can reach the person managing the list at [email protected] When replying, please edit your Subject line so it is more specific than "Re: Contents of phenixbb digest..." Today's Topics: 1. Re: Structure with high clashscore ([email protected]) 2. Re: Structure with high clashscore (Pavel Afonine) 3. Deadline Extended: Macromolecular Crystallography - CSHL Course October 2025 (Paul Adams) 4. Phenix LigandFit RSCC calculation questions (Theo Teng) 5. Re: Phenix LigandFit RSCC calculation questions (Bernhard Rupp) ---------------------------------------------------------------------- Message: 1 Date: Tue, 22 Jul 2025 15:09:07 -0000 From: [email protected] Subject: [phenixbb] Re: Structure with high clashscore To: [email protected] Message-ID: <[email protected]> Content-Type: text/plain; charset="utf-8" Hi, one more possibility - we find that if the structure is refined without hydrogens, but one or more ligands do have hydrogens (not intentionally), then Molprobity adds hydrogens to all residues and clashscore calculated by it (now including hydrogens) jumps a lot. The remedy would be to delete all hydrogens from the structure before the refinement (or refine with hydrogens added everywhere). Best Leonid JEROME JOHNSON wrote:

Hello all,

I'm happy to join the forum! I have a problem with clashscores and would be grateful for support.

I have diffraction data for a 3HP-CoA Synthetase from N. maritimus resolved to 2.7 Angstroms. For MD, I used an alphafold structure (as I understand commonly results in high clashscore values) and after numerous rounds of refinement, the clashscore remains high at 11. I recently tried using gromacs to energy minimize and got values of 5 and 3 (according to molprobity), but after refinement these values immediately jumped back up to ~30.

I wondered if you could describe the best way to reduce these?

Attached is my latest round of refinement should you wish to take a look!

Best, Jerome

------------------------------ Message: 2 Date: Tue, 22 Jul 2025 10:29:20 -0500 From: Pavel Afonine Subject: [phenixbb] Re: Structure with high clashscore To: [email protected], [email protected] Message-ID: Content-Type: text/plain; charset=UTF-8; format=flowed Hi All,

Hi, one more possibility - we find that if the structure is refined without hydrogens, but one or more ligands do have hydrogens (not intentionally), then Molprobity adds hydrogens to all residues and clashscore calculated by it (now including hydrogens) jumps a lot. The remedy would be to delete all hydrogens from the structure before the refinement (or refine with hydrogens added everywhere).

this is an interesting observation. MolProbity always adds all H to compute clashscore -- one can't compute clashscore without H present. I suspect having H on ligands only triggers it to 'think' that H are already present, and it computes clashscore without adding H to everything else. Could you please send me the file off list (the one that has H only on the ligand)? I think we better investigate this..

...

I'm happy to join the forum! I have a problem with clashscores and would be grateful for support.

I have diffraction data for a 3HP-CoA Synthetase from N. maritimus resolved to 2.7 Angstroms. For MD, >> commonly results in high clashscore values) and after numerous rounds of refinement, the clashscore remains high at 11.

Dear Phenix developers,

I hope this message finds you well.

We had two specific questions about how the real-space correlation coefficient (RSCC) is computed when using Phenix.LigandFit:

1. What radius is used around the ligand or search center when calculating the RSCC during ligand fitting? Is this radius fixed or adaptive?

2. Which CCTBX function(s) underlie the RSCC calculation used in LigandFit?

We aim to compare the placements from LigandFit to other ligand

11 looks just fine. Note, clashscore=0 is not the goal because clashscore does not account for non-standard links and for example, can count as a severe clash atoms involved into nonstandard links, and similar. In Phenix Comprehensive Validation, go over the table of clashes, they are sorted, worst first, and check and try to address top few worst offenders. Pavel ------------------------------ Message: 3 Date: Tue, 22 Jul 2025 10:52:38 -0700 From: Paul Adams Subject: [phenixbb] Deadline Extended: Macromolecular Crystallography - CSHL Course October 2025 To: [email protected], [email protected] Message-ID: <[email protected]> Content-Type: text/plain; charset=utf-8 Dear Colleagues, For those of you that may have missed the deadline, the application deadline has been extended to August 1st. A reminder that the Cold Spring Harbor Macromolecular Crystallography course will take place October 12-28th this year (pleased see below for more details). This comprehensive course is an outstanding place to learn both the theoretical and practical aspects of macromolecular crystallography. There are extensive lectures and practical sessions from world recognized experts in crystallization, data collection, data processing, structure solution, refinement, and validation. The goal of the course is for researchers who have had some exposure to structural biology to become experts in crystallography. This is an experience in macromolecular crystallography learning that cannot be found anywhere else, and the student/teacher ratio is often 1:1. Please follow this link to the course web site: https://meetings.cshl.edu/courses.aspx?course=C-CRYS In particular, please note the information about the various fellowships, scholarships, and stipends that are available. Most applicants ultimately receive some form of financial support. If anyone has any questions please send me an e-mail, and we will be happy to answer all queries. Paul Adams  -- Paul Adams (he/him/his) Associate Laboratory Director for Biosciences, LBL (https://biosciences.lbl.gov) Principal Investigator, Computational Crystallography Initiative, LBL (http://cci.lbl.gov) Vice President for Technology, the Joint BioEnergy Institute (http://www.jbei.org) Principal Investigator, ALS-ENABLE, Advanced Light Source (http://als-enable.lbl.gov) Laboratory Research Manager, ENIGMA Science Focus Area (http://enigma.lbl.gov) Adjunct Professor, Department of Bioengineering, UC Berkeley (http://bioeng.berkeley.edu) Member of the Graduate Group in Comparative Biochemistry, UC Berkeley (http://compbiochem.berkeley.edu) Building 91, Room 410 Building 978, Room 4126 Tel: 1-510-486-4225 http://cci.lbl.gov/paul ORCID: 0000-0001-9333-8219 Lawrence Berkeley Laboratory 1 Cyclotron Road BLDG 91R0183 Berkeley, CA 94720, USA. Executive Assistant: Michael Espinosa [ [email protected] ][ 1-510-333-6788 ] Phenix Consortium: Ashley Dawn [ [email protected] ][ 1-510-486-5455 ] -- ------------------------------ Message: 4 Date: Tue, 29 Jul 2025 14:34:52 -0400 From: Theo Teng Subject: [phenixbb] Phenix LigandFit RSCC calculation questions To: [email protected] Message-ID: Content-Type: text/plain; charset="UTF-8" Dear Phenix developers, I hope this message finds you well. We had two specific questions about how the real-space correlation coefficient (RSCC) is computed when using Phenix.LigandFit: 1. What radius is used around the ligand or search center when calculating the RSCC during ligand fitting? Is this radius fixed or adaptive? 2. Which CCTBX function(s) underlie the RSCC calculation used in LigandFit? We aim to compare the placements from Lig-- *Theodore W. Teng* Harvard College | Class of 2027 A.B. student in Chemical and Physical Biology Secondary in Global Health and Health Policy ------------------------------ Message: 5 Date: Tue, 29 Jul 2025 11:38:27 -0700 From: Bernhard Rupp Subject: [phenixbb] Re: Phenix LigandFit RSCC calculation questions To: Theo Teng Cc: [email protected] Message-ID: Content-Type: text/plain; charset="UTF-8" There is a modified quote from a famous statistician, which one might keep in mind on such ventures: All ligands are wrong, but some are useful. Cheers, BR ------------------------------------------------------ Bernhard Rupp https://www.hofkristallamt.org/ [email protected] [email protected] +1 925 209 7429 +43 676 571 0536 ------------------------------------------------------ People can be divided into three classes: The few who make things happen; The many who watch what is happening; and the overwhelming majority who have no clue what is happening. ------------------------------------------------------ On Tue, Jul 29, 2025 at 11:35 AM Theo Teng wrote: placement

methods, and your response would be appreciated.

Best regards, --

*Theodore W. Teng* Harvard College | Class of 2027 A.B. student in Chemical and Physical Biology Secondary in Global Health and Health Policy _______________________________________________ phenixbb mailing list -- [email protected] To unsubscribe send an email to [email protected] Unsubscribe: phenixbb-leave@%(host_name)s

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