March 2026 - phenixbb - phenix-online.org

Re: coot-1 linked to phenix
by Roberto Steiner 06 Apr '26

06 Apr '26

Hi Chiara I have installed coot-1 using homebrew and using /opt/homebrew/Cellar/coot/1.1.20/bin/coot works for me. Ciao Roberto Roberto A Steiner www.steinerlab.org https://twitter.com/steiner_lab roberto.steiner(a)kcl.ac.uk Randall Centre for Cell and Molecular Biophysics Faculty of Life Sciences and Medicine King's College London Room 3.10A New Hunt's House, Guy's Campus SE1 1UL, London, UK Phone 0044 20 78488216 Fax 0044 20 78486435 roberto.steiner(a)unipd.it Dipartimento di Scienze Biomediche Università degli Studi di Padova Viale G. Colombo 3 35131 Padova, Italia Telefono 0039 049 8276409 Responses to emails are not expected outside of your normal working hours. On 28/01/2026, 13:27, "Rapisarda, Chiara /FR via phenixbb" <phenixbb(a)phenix-online.org <mailto:[email protected]>> wrote: Hello, I have a Mac that I upgraded to Tahoe, and now coot 0.9 isn’t working any more. I would like to link phenix to coot-1. I can do that by adding: /Applications/ccp4-9/coot_py3/bin/coot To the coot path in preferences, but after a refinement when I open coot , it is open but it is not connected to the phenix refine job and no PDB nor map is open. I am aware that I can manually open the map and pdf, I would like to know if coot-1 can be opened in a way that will allow me to navigate the structure using phenix. When I ask gemini it tells me that I should point it to: /Applications/ccp4-9/bin/coot-py3 But it doesn’t exist in my ccp4 installation. Has anyone successfully managed to link coot-1 to phenix using a good bridge? Any help will be greatly appreciated. Best, Chiara _______________________________________________ phenixbb mailing list -- phenixbb(a)phenix-online.org <mailto:[email protected]> To unsubscribe send an email to phenixbb-leave(a)phenix-online.org <mailto:[email protected]> Unsubscribe: phenixbb-leave@%(host_name)s

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Issues refining a cyclic peptide with non-natural residues
by Dayna Louise Holroyd 31 Mar '26

31 Mar '26

Hi all, I am currently refining a cyclic peptide which I have modelled into my 3A crystal structure. The peptide contains multiple non-natural amino acids, two of which haven't been defined in the PDB before by a three letter code (made cif files with elbow for these). I have been adding custom restraint files each refinement round to connect residues at the ends and maintain cyclisation. I am encountering various issues during refinement: 1. Certain pairs of non-natural residues drift apart after refinement if I do not include restraints between the two residues. 2. Some backbone dihedral angles are much smaller than expected, while other angles appear unusual or physically implausible, even after defining particular angles in the restraint files. I suspect that some of these issues may be related to the compact nature of the cyclic peptide and the presence of undefined residues, but I am unsure how to address them effectively. Has anyone refined similar cyclic peptides with non-natural residues and can offer advice on my problems with restraints, compact backbone angles, non-natural residues, etc? Any guidance or ideas would be greatly appreciated. Many thanks, Dayna Holroyd PhD Candidate Protein Crystallography and Structural Biology Laboratory School of Biological Sciences | College of Science ADELAIDE UNIVERSITY

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Industrial Biostructures America conference 2026
by Xu, Rui [JRDUS] 27 Mar '26

27 Mar '26

The Industrial Biostructures America conference will take place on May 11 & 12, 2026 at the Sanofi Cambridge Crossing site in Cambridge MA. The conference was launched in 2018 to bring the industry-based structural biology community together for two days of presentations and networking. This is a great place for industrial structural biologists, as well as those who are industry-curious. The conference will feature keynote presentations by: * Dr. Sandra Gabelli - Global Head of Protein and Structural Chemistry at Merck * Dr. Derek Lowe - Director in Chemical Biology at Novartis and author of widely-read science and industry web site "In the Pipeline" Conference information is available at https://industrialbiostructuresamerica.org<https://industrialbiostructuresamerica.org/> along with guidelines for submitting abstracts for scientific presentations during the conference. Scientific sessions will cover the following topics: * Membrane Proteins, chaired by Dr. Elena Levin (UCB) * Conformational dynamics (allostery), chaired by Dr. Rui Xu (J&J) * Fragments and Proximity, chaired by Dr. Kerren Swinger (Takeda) * Tools of the Trade and Cryo-EM, chaired by Dr. Eva Cunha (Proteros) * Biologics, chaired by Dr. Joe Batchelor (Sanofi) * AI/ML in Drug Discovery and the Future of Structural Biology, chaired by Dr. Jill Chrencik (Merck) We also plan on a panel discussion on the topic of "Frontiers in Structural Biology for Drug Discovery and Development" The abstract deadline is April 1. Space is limited so if you're interested, please register soon. Contact us at iba(a)proteros.com<mailto:[email protected]> for additional information

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How to do map sharpening?
by Francisco 25 Mar '26

25 Mar '26

Hi... I am trying to sharpen a map (x-ray) with the new phenix.auto_sharpen -> phenix.map_sharpening program. Got a script that basically runs phenix.xtriage to get the fraction of solvent content and some things and then I do ... ``` phenix.map_sharpening \ sharpening_method=b-factor \ mtz_in="$MTZ_IN" \ map_coeff_labels="2FOFCWT,PH2FOFCWT" \ map_model.model="$PDB_IN" \ crystal_info.resolution="$RESOL" \ b_factor_sharpening.b_factor_sharpening_crystal_info.solvent_content="$SOLVENT" \ b_factor_sharpening.b_factor_sharpening_crystal_info.is_crystal=True \ > sharpen.log 2>&1 ``` The problem is that I cannot open the mtz file in coot (mtz dump is attached) ... BUT ... I can open the sharpened map (ccp4 format) ... BUT ... the map is not covering the protein completely.. How do I do that? (1.png 2.png just showing the limits of the map) In gui mode I do get the map over the protein...BUT I cannot select the "FOFCWT,PHFOFCWT" labels (3.png ... That's the second part of the plan...) I am using phenix-dev 5989 Thanks a lot for your help

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Re: Monomer of dimer?
by Andrea Smith 25 Mar '26

25 Mar '26

Hi Liu, we had a case in our lab where we had one molecule in the ASU even for a swapped dimer, so it is possible to have one molecule in the asymmetric unit even if your protein is a dimer. I would think that your problem might be somewhere else. Did you check with Xtriage if it can flag some issues with the data? Andrea On Wednesday, March 25, 2026 07:31 CET, "princeadam(a)163.com" <princeadam(a)163.com> wrote: Dear PhenixBB community, I am currently working on solving the structure of protein X (110 amino acids). The protein forms a dimer in solution, and dimerization is functionally relevant. Based on initial analysis, the asymmetric unit (ASU) was estimated to contain one copy [unit cell: 82.699, 82.699, 36.435, 90 , 90, 120]. The data extend to 1.2 Å resolution, but the final R factors are around 0.23/0.25, which seem higher than expected at this resolution, and we have not been able to improve them further. When I examined the structure using symmetry mates in PyMOL, I observed a clear dimer that appears biologically meaningful. This makes me suspect that the ASU estimation might be incorrect—especially for a small protein like this, the ASU could potentially contain a dimer rather than a monomer. However, every time I use a dimer model as the search model for molecular replacement, Phaser consistently returns a monomer solution. I would greatly appreciate any suggestions on how to successfully obtain the dimeric model that matches the crystallographic symmetry. Thank you in advance for your help! Best regards, Liu _______________________________________________ phenixbb mailing list -- phenixbb(a)phenix-online.org To unsubscribe send an email to phenixbb-leave(a)phenix-online.org Unsubscribe: phenixbb-leave@%(host_name)s

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How to start the Phenix Coot Implementation manually
by Biertuempfel, Christian (NIH/NHLBI) [E] 20 Mar '26

20 Mar '26

Dear all, Is there a clever way how to start the coot implementation from phenix manually? Basically, I am running phenix on one machine and I would like to open coot on another. I tried to copy/import my phenix database and project files on the “coot machine" but the paths are not properly imported. Which files are read when clicking “Open in Coot” in the GUI? Can I somehow run “Open in Coot” from the command line? Thanks, christian

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Test message sorry for the noise
by Nigel Moriarty 20 Mar '26

20 Mar '26

Cheers Nigel --- Nigel W. Moriarty Building 91, Molecular Biophysics and Integrated Bioimaging Lawrence Berkeley National Laboratory Berkeley, CA 94720-8235 Email : NWMoriarty(a)LBL.gov Web : CCI.LBL.gov ORCID : orcid.org/0000-0001-8857-9464

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unrealistic low clashscore in phenix.refine
by Kevin M Jude 18 Mar '26

18 Mar '26

I’m using phenix 2.0-5936 on my M1 Mac. I notice in phenix.refine that the run status reports a realistic clashscore (7.5) for my structure, but in the Molprobity tab of phenix.refine the reported clashscore is 0.77, with only 4 clashes identified with a maximum overlap of 0.472 Å. Running Comprehensive Validation (X-rayNeutron) gives a full list of 76 overlapping pairs, maximum overlap 0.705 Å, and a clashscore of 7.65. -- Kevin Jude, PhD Structural Biology Research Specialist, Garcia Lab Howard Hughes Medical Institute Stanford University School of Medicine Beckman B177, 279 Campus Drive, Stanford CA 94305

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CBMS - Lecture Series - Serganov
by Stojanoff, Vivian 18 Mar '26

18 Mar '26

Dear Colleagues, you are cordially invited to join the Center for Biomolecular Structure Lecture Series ……….. Alexander A. Serganov Associate Professor, Department of Biochemistry and Molecular Pharmacology NYU Grossman School of Medicine NYU Langone Health WEDNESDAY, March 25, 13:30 (EST) "Redefining dogmas in bacterial physiology: the case of mRNA” Register in advance for this meeting: https://bnl.zoomgov.com/meeting/register/QkF6wZmvRJCTtT9RG0djuw Time conversion Link: https://www.worldtimebuddy.com/<https://urldefense.com/v3/__https:/gcc02.safelinks.protection.outlook.com/?…> Abstract: The degradation of mRNA plays a crucial role in determining the number of mRNA molecules and, consequently, influences the yield of protein biosynthesis across all organisms. While the regulation of mRNA lifetime is well-recognized as vital for gene expression in eukaryotes, it has long been assumed that bacteria lack sophisticated mechanisms for regulating mRNA stability and degradation. Our findings challenge this assumption, revealing that bacterial mRNAs possess unexpected properties and employ molecular mechanisms that rival in complexity those in eukaryotic systems. ================= Vivian Stojanoff, PhD Education, Training, Outreach User Program p 1(631) 344 8375 e lifescience(a)bnl.gov<mailto:[email protected]> w https://www.bnl.gov/ps/lifesciences/<https://www.bnl.gov/ps/lsbr/> Address: Center for Biomolecular Structure National Synchrotron Light Source II Building 745 Brookhaven National Laboratory Upton NY 11973

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Matplotlib error for 2.0-5936
by matthew.belousoff＠monash.edu 15 Mar '26

15 Mar '26

Hey guys, Few details first: OS: Linux Mint 22.1 Kernel: 6.8.0-71 Phenix Build: Phenix-2.0-5936-CUDA12-Linux-x86_64 Generally everything works fine, but when I run a RealSpace refinement job, afterwards going through the diagnostic details is quite slow and the console keeps printing out: findfont: Font family 'Courier' not found. findfont: Font family 'Monaco' not found. findfont: Font family 'Helvetica' not found. This seems like a matplotlib error to me. I will note that I didn't get these errors with any older versions of phenix on the same system. cheers, matt B

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