April 2026 - phenixbb - phenix-online.org

real space refinement with a reference model
by Valérie Biou 29 Apr '26

29 Apr '26

Dear all, I would like to use a reference model to try to improve my cryo-em refinement geometry. I have an AF3 model that superposes with an RMSD of 1.4Å wrt my structure, and I renumbered the residues so they match with my structure. however, I get the message Reference Model Matching Summary: reference file: renumbered.pdb Model: Reference: Total # of matched residue pairs: 0 Total # of reference model restraints: 0 input file list (truncated from the root) default_model = "RealSpaceRefine_72/rsr71_isolde1_real_space_refined_072.pdb" real_map_files = /cryosparc_P29_J343_010_volume_map_sharp.mrc" default_real_map = cryosparc_P29_J343_010_volume_map_sharp.mrc" restraint_files = eLBOW_46/elbow.P.P_pdb.001.cif" default_restraint = eLBOW_46/elbow.P.P_pdb.001.cif" phil_files = Phenix/.phenix/project_data/real_space_refine_88.eff" default_phil = Phenix/.phenix/project_data/real_space_refine_88.eff" then : reference_model { enabled = True file = "renumbered.pdb" side_chain = False secondary_structure_only = True search_options { chain_max_rmsd = 3.0 Can you please help me with this? Kind regards Valérie

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refining HO2' atoms
by p.auffinger＠unistra.fr 29 Apr '26

29 Apr '26

Hi all, Is there an easy way to only refine hydroxyl atoms (like ribose HO2' atoms) in Phenix.refine ? I understand that it can be done in readySet. Thanks, Pascal

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Riding hydrogens
by p.auffinger＠unistra.fr 27 Apr '26

27 Apr '26

Dear all, I am trying to refine a high-resolution cryo-EM structure. However, some of the guanine NH2 groups end up out of plane (I used cdl). Is that an expected behavior ? It seems that may be planarity restraints associated with hydrogens are not strong enough. Is there an option to augment them ? May be also the riding option only involves distance and angle restraints ? This is not clear from the manual to me. Also, for OH groups like ribose 2'-OH groups, I assume that the riding option only involves distance restraints and that these H-atoms are otherwise free to rotate Can you please help me out here ? Thanks, Pascal

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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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