- phenixbb - phenix-online.org

Large project database = slow opening of Phenix GUI?
by Harry Mark Greenblatt 26 Apr '26

26 Apr '26

BS”D Hi all, Has anybody experienced slow opening of the Phenix GUI, when a person has amassed well over a decade worth of projects, or should that not affect the startup speed? Thanks Harry -------------------------------------------------------------------- Harry M. Greenblatt Associate Staff Scientist Dept of Chemical and Structural Biology harry.greenblatt(a)weizmann.ac.il<mailto:[email protected]> Weizmann Institute of Science Phone: 972-8-934-6340 234 Herzl St. Facsimile: 972-8-934-3361 Rehovot, 7610001 Israel

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Unable to open phenix.refine
by p.r.tiley＠pgr.reading.ac.uk 20 Apr '26

20 Apr '26

Has anyone had problems trying to open phenix.refine? I have installed Phenix 2.0.5936 several times but keep on getting the following error message when I click on phenix.refine: KeyError : 'Unrecognized input file parameter refinement.gui.migration.refinement.input.sequence.file_name (allowed: data_manager.model.file, refinement.reference_model.file, refinement.gui.migration.refinement.input.pdb.file_name, refinement.gui.migration.refinement.input.pdb.neutron_file_name, refinement.gui.migration.refinement.input.pdb.electron_file_name, refinement.den.reference_file).' Any help/advice would be much appreciated. Thanks in anticipation!

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by cory84522＠gmail.com 09 Apr '26

09 Apr '26

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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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ReadySet and cif
by p.auffinger＠unistra.fr 02 Apr '26

02 Apr '26

Hi, Is it possible to get a cif file as an output when using the ReadySet gui ? What is "Output file base" ? If I precise "output.cif" the program seems not to be happy ! Thanks, Pascal

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Hydrogens on modified residues -- ReadySet
by p.auffinger＠unistra.fr 02 Apr '26

02 Apr '26

Dear all, ReadySet encounters some issues when adding hydrogens to modified residues. I used the 7k00 ribosome structure as a test. I noticed missing hydrogens on G7M, 4OC, UR3, MA6, 6MZ, 2MA, OMU, 2MG. Additionally, hydrogens are missing on IAS and on the NH groups of D2T, MS6 and 4D4. An amino hydrogen is also missing on 4D4. When using Coot on this file, everything looks much better except that some hydrogens are added to amino acid backbones of modified residues that need to be removed by hand. Any ideas ? Thanks a lot, Pascal

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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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