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Phenix Phaser Question
by hyun4867 11 Jul '23

11 Jul '23

Dear, Everyone Hi all, I am Hyun Jeong. I want to ask you about phenix phaser problem. I obtain diffraction pattern of crystal that is complex. I tried to solve the phase based on the Apo structure i previoulsy solved. Using full-featured phaser, i obtain 18 Phaser solution. This is really strange number. But, the map obtained 18 Phaser solution is fitted in electron density map. May I proceed with processing using the discovered electron map with 18 Phasers? Is it necessary to redo the scaling? I appreciate your request for advice. Best regards, Hyun Jeong

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symmetry finding question
by Dmitry Semchonok 07 Jul '23

07 Jul '23

Dear colleagues, I have a chaperone map with D7 symmetry. But the Phenix «Map symmetry» tool finds only C7. Is there a way to make the software see the D7 symmetry of my protein? Many thanks for considering my request. Sincerely, Dmitry

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Discrepancy between Phenix GUI and command line for MR
by Xavier Brazzolotto 05 Jul '23

05 Jul '23

Dear Phenix users I’ve noticed that molecular replacement was clearly slower while running from the GUI compared to using the command line (phenix.phaser). Did you also observe such behavior? Best Xavier

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General interest, education article
by John R Helliwell 05 Jul '23

05 Jul '23

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Young Crystallographers Meeting in Strasbourg
by Triantafyllidis, Dimitrios P. 30 Jun '23

30 Jun '23

Dear all, We are pleased to announce that the first joint Franco-German Young Crystallographers's Meeting (YCM1) will be held from September 26-29 in Strasbourg. The collaboration of the French and German crystallographic associations and the IB-ID doctoral college will bring a bi-national and international dimension, with the opportunity for participants to present their work in English, either orally (over thirty slots available) or in poster form. The deadline for abstract submission is July 15. The scientific committee, mainly made up of young researchers, is preparing a rich, multidisciplinary program, including meetings with industrialists working in the field of crystallography. We will be delighted to welcome a prestigious guest in the person of Professor Jean-Pierre Sauvage, winner of the 2016 Nobel Prize in Chemistry. Other guests will be announced shortly on our website: https://ycm1.xyz Full details of the spirit of the event and practical details are available online. A special effort has been made to offer very attractive registration fees (140 EUR) including meals and accommodation. This offer is limited to the first 50 registrants, so don't delay your registration! For any question, feel free to contact us at: ycm1.communication(a)gmail.com Please spread the word around, especially to our young colleagues, and we look forward to seeing you in the beautiful city of Strasbourg this autumn! On behalf of the YCM1 organizing committee, Dimitris Triandafillidis ______________________________ Dimitris P. Triandafillidis Hamburg Centre for Ultrafast Imaging Universität Hamburg HARBOR (Building 610) Luruper Chaussee 149, DE-22761 Hamburg, Germany

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Apply NFC operators to get identical 14 homo oligomeric model
by Dmitry Semchonok 29 Jun '23

29 Jun '23

Dear colleagues, I use the «Apply NFC operators» tool and would like to use the option described under the "Configuration" sign. But when I follow these instructions, the outcome model is still a single subunit. Initially, I want to get 14mer (with D7 symmetry) with identical 14 monomers. Could you please prompt how to get it with the «Apply NF operators»? Additionally, the resulting model doesn't contain description information in the newly created PDB file. Would you happen to know how to get the correct PDB file? Thanks in advance. Kind regards, Dmitry

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Postdoctoral position in method development (York Structural Biology Laboratory)
by Jon Agirre 27 Jun '23

27 Jun '23

Dear all, Applications are invited for a Postdoctoral Research Associate position, funded by the Royal Society, for up to 30 months to work with Dr Jon Agirre in the Department of Chemistry. The successful applicant will join a vibrant team of researchers at the heart of the world-leading York Structural Biology Laboratory (YSBL). The work of the laboratory over the years has included the delivery of world-leading methods and experimental discoveries, training and nurturing hundreds of outstanding scientists in the process. Role The AlphaFold software for protein model prediction has revolutionised workflows in structural biology. However, while high-accuracy models are now available for most human proteins of medical relevance, up to 50% of those proteins are expected to be glycosylated – a modification whose structure AlphaFold does not predict. Protein glycosylation is greatly important, with implications for protein folding and molecular recognition including, as evidenced by the spike glycoprotein of SARS-CoV-2, viral infection. In collaboration with other scientists, we have extended the Privateer software to interactively build missing glycosylation onto precalculated AlphaFold models. In parallel, we have developed analyses that allow us to get a clear picture of glycans and their interactions, including H-bonds and XH-Pi interactions. We expect that these methods will enable us to, based on existing glycobiological knowledge, extend the Privateer software to automatically complete AlphaFold models with crucial missing glycosylation components. We are seeking a person with an interest in both biology and coding, who can collaborate with others in a very diverse team with a mission to further our knowledge of glycobiology and seize the opportunities presented by a deeper understanding of it. Main duties and responsibilities To develop and extend the Privateer software to complete AlphaFold models with the missing glycan components. To further our existing collaborations with CCP4, CCP-EM, PDB-REDO, the Protein Data Bank and the AlphaFold Protein Structure Database. Department The Department of Chemistry is one of the largest and most successful departments at York and we are renowned internationally for our research. As a department, we strive to provide a working environment that allows all staff and students to contribute fully, to flourish, and to excel. We are proud of our Athena Swan Gold Award. The Department of Chemistry values all employees for the qualities and skills they bring to the workplace and aims to be a diverse and egalitarian community in which all can thrive. For informal enquiries: please contact Dr Jon Agirre, jon.agirre(a)york.ac.uk To apply: https://jobs.york.ac.uk/vacancy/research-associate-529961.html Deadline for applications: 20 August 2023. Many thanks for making it this far in the advert! With best wishes, Jon -- Dr Jon Agirre Royal Society University Research Fellow (assistant professor) CCP4 WG2 co-chair | instruct-ERIC representative @ 3D-Bioinfo SC (Elixir) York Structural Biology Laboratory, Department of Chemistry University of York, Heslington, YO10 5DD, York, UK

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problems in running Phenix
by Gianluca Cioci 27 Jun '23

27 Jun '23

Dear All, I am experiencing difficulties in installing Phenix in my Linux system based on Ubuntu 20.04.6 LTS (GNU/Linux 5.15.0-75-generic x86_64) Installation is completed, but when I try tu run phenix I get the message: 12:57:27: Cannot set locale to language "English". 12:57:27: locale 'en_GB' cannot be set. and in the terminal I get: Error in sys.excepthook: Traceback (most recent call last): File "/data/software/phenix/phenix-1.20.1-4487/modules/phenix/wxGUI2/App.py", line 898, in _excepthook Error.show_exception_dialog(type, value, traceback) File "/data/software/phenix/phenix-1.20.1-4487/modules/phenix/wxGUI2/Error.py", line 76, in show_exception_dialog if (app.bug_timer.IsRunning() is False): AttributeError: 'PhenixApp' object has no attribute 'bug_timer' Original exception was: Traceback (most recent call last): File "/data/software/phenix/phenix-1.20.1-4487/build/../modules/phenix/wxGUI2/command_line/main.py", line 23, in <module> run(sys.argv[1:]) File "/data/software/phenix/phenix-1.20.1-4487/build/../modules/phenix/wxGUI2/command_line/main.py", line 17, in run wxapp = App.PhenixApp(args) File "/data/software/phenix/phenix-1.20.1-4487/modules/phenix/wxGUI2/App.py", line 74, in __init__ wx.App.__init__(self, 0) File "/data/software/phenix/phenix-1.20.1-4487/conda_base/lib/python2.7/site-packages/wx-3.0-gtk2/wx/_core.py", line 8628, in __init__ self._BootstrapApp() File "/data/software/phenix/phenix-1.20.1-4487/conda_base/lib/python2.7/site-packages/wx-3.0-gtk2/wx/_core.py", line 8196, in _BootstrapApp return _core_.PyApp__BootstrapApp(*args, **kwargs) File "/data/software/phenix/phenix-1.20.1-4487/modules/phenix/wxGUI2/App.py", line 108, in OnInit show_splash_screen(timeout=2000) File "/data/software/phenix/phenix-1.20.1-4487/modules/phenix/wxGUI2/App.py", line 952, in show_splash_screen dlg,-1,citations.format_citation(citations.citations_db.get("phenix"))) File "/data/software/phenix/phenix-1.20.1-4487/conda_base/lib/python2.7/site-packages/wx-3.0-gtk2/wx/_controls.py", line 997, in __init__ _controls_.StaticText_swiginit(self,_controls_.new_StaticText(*args, **kwargs)) UnicodeDecodeError: 'ascii' codec can't decode byte 0xc3 in position 40: ordinal not in range(128) Anyone has a working solution for this ? We have tried to change the locale to en_GB, but still it's not working. With many thanks, GIA -- Dr. Gianluca CIOCI Toulouse Biotechnology Institute (TBI) https://www.toulouse-biotechnology-institute.fr/en/poles/equipe-cimes/ PICT - Plateforme Intégrée de Criblage de Toulouse http://www.pict.ipbs.fr/ Tel: +33 (0)5 61 55 97 68 E-mail: cioci(a)insa-toulouse.fr TBI - INSA Toulouse 135 avenue de Rangueil 31077 Toulouse CEDEX 04 http://www.toulouse-biotechnology-institute.fr

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Refining peptides with beta-amino acids
by Bram Mylemans 27 Jun '23

27 Jun '23

Dear experts, I’m trying to refine a crystal structure of a peptide that contains some beta-amino acids. I have tried generating restraints with elbow from a sdf file. I changed the naming of the atoms to conform with the protein naming and added the L-peptide linking tag. This seems to work for refining and also local refine in coot works. However, the peptide bond is not kept planar. Does anyone have an idea how to make sure the amide bond is correctly constrained? I have included the restrained file I made for L-beta-Leucine below for reference. Best wishes, ---------- Dr. Bram Mylemans Post-doctoral Research Associate Woolfson group School of Chemistry University of Bristol # electronic Ligand Builder and Optimisation Workbench (eLBOW) # - a module of PHENIX version 1.20.1-4487- # - file written: Sun May 14 14:31:25 2023 # # Inital geometry file: a 60 line input string # Ligand name: (3S)-3-amino-5-methylhexanoic acid # Quantum optimisation: True # Method: uhf # Random seed: 3628800 # SMILES string: CC(C)C[C@H](N)CC(O)=O # data_comp_list loop_ _chem_comp.id _chem_comp.three_letter_code _chem_comp.name _chem_comp.group _chem_comp.number_atoms_all _chem_comp.number_atoms_nh _chem_comp.desc_level B3L B3L '(3S)-3-amino-5-methylhexanoic acid' L-peptide 24 10 . # data_comp_B3L # loop_ _chem_comp_atom.comp_id _chem_comp_atom.atom_id _chem_comp_atom.type_symbol _chem_comp_atom.type_energy _chem_comp_atom.charge _chem_comp_atom.partial_charge _chem_comp_atom.x _chem_comp_atom.y _chem_comp_atom.z B3L O O O 0 -0.621 -0.0468 -0.0672 0.0379 B3L C C C 0 0.403 1.2030 -0.0409 -0.0524 B3L CA C CH2 0 -0.215 2.0004 0.0099 1.2717 B3L CB C CH1 0 0.109 1.5936 -1.1463 2.1941 B3L N N NH2 0 -0.452 2.4198 -2.3233 1.9111 B3L CG C CH2 0 -0.173 1.7636 -0.6462 3.6485 B3L CD C CH1 0 -0.040 1.5804 -1.7407 4.6994 B3L CE2 C CH3 0 -0.160 1.9937 -1.1916 6.0651 B3L CE1 C CH3 0 -0.159 0.1402 -2.2497 4.7124 B3L HA H HCH2 0 0.055 3.0941 0.0115 1.0876 B3L HAA H HCH2 0 0.036 1.7870 0.9871 1.7352 B3L HB H HCH1 0 0.088 0.5145 -1.4120 2.0199 B3L HN H HNH2 0 0.153 1.9179 -3.1939 1.9355 B3L HG H HCH2 0 0.049 2.7650 -0.1815 3.7540 B3L HGA H HCH2 0 0.063 1.0542 0.1844 3.8432 B3L HD H HCH1 0 0.048 2.2575 -2.6020 4.4708 B3L H3E2 H HCH3 0 0.033 2.4606 -1.9617 6.6915 B3L H2E2 H HCH3 0 0.049 2.7302 -0.3796 5.9910 B3L H1E2 H HCH3 0 0.045 1.1543 -0.7788 6.6358 B3L H3E1 H HCH3 0 0.045 0.0304 -3.1957 4.1675 B3L H2E1 H HCH3 0 0.034 -0.2410 -2.4354 5.7240 B3L H1E1 H HCH3 0 0.068 -0.5687 -1.5528 4.2450 B3L OXT O OC -1 -0.606 1.8564 -0.0003 -1.1279 B3L HNA H HNH2 0 0.147 3.2587 -2.3840 2.4671 # loop_ _chem_comp_bond.comp_id _chem_comp_bond.atom_id_1 _chem_comp_bond.atom_id_2 _chem_comp_bond.type _chem_comp_bond.value_dist _chem_comp_bond.value_dist_esd B3L C O single 1.253 0.015 B3L C OXT single 1.259 0.016 B3L CA C single 1.546 0.037 B3L CB CA single 1.534 0.036 B3L CB HB single 1.125 0.040 B3L N CB single 1.466 0.036 B3L N HNA single 1.008 0.037 B3L CG CB single 1.547 0.037 B3L CG HG single 1.109 0.039 B3L CD CG single 1.528 0.035 B3L CD CE1 single 1.528 0.035 B3L CE2 CD single 1.529 0.035 B3L CE2 H1E2 single 1.096 0.038 B3L CE1 H1E1 single 1.098 0.038 B3L CE1 H3E1 single 1.097 0.038 B3L HA CA single 1.109 0.037 B3L HAA CA single 1.102 0.040 B3L HN N single 1.005 0.037 B3L HGA CG single 1.110 0.039 B3L HD CD single 1.119 0.040 B3L H3E2 CE2 single 1.097 0.038 B3L H2E2 CE2 single 1.099 0.038 B3L H2E1 CE1 single 1.097 0.038 # loop_ _chem_comp_angle.comp_id _chem_comp_angle.atom_id_1 _chem_comp_angle.atom_id_2 _chem_comp_angle.atom_id_3 _chem_comp_angle.value_angle _chem_comp_angle.value_angle_esd B3L OXT C CA 117.56 2.401 B3L CA C O 116.95 2.270 B3L OXT C O 125.42 1.837 B3L HAA CA HA 105.03 2.935 B3L HAA CA CB 111.34 2.722 B3L HA CA CB 111.25 2.583 B3L HAA CA C 106.82 2.670 B3L HA CA C 111.50 2.415 B3L CB CA C 110.69 2.417 B3L HB CB CG 109.11 2.657 B3L CG CB N 112.27 2.657 B3L HB CB N 108.74 2.657 B3L CG CB CA 107.01 2.247 B3L N CB CA 109.86 2.386 B3L HB CB CA 109.83 2.388 B3L HNA N HN 110.49 3.000 B3L HN N CB 114.17 2.677 B3L HNA N CB 114.27 2.682 B3L HGA CG HG 104.29 2.953 B3L HGA CG CD 109.80 2.649 B3L HG CG CD 110.06 1.813 B3L HGA CG CB 109.67 2.659 B3L CD CG CB 113.69 2.657 B3L HG CG CB 108.91 2.671 B3L HD CD CE1 108.40 2.672 B3L HD CD CE2 107.17 2.674 B3L CE1 CD CE2 111.53 2.389 B3L HD CD CG 109.76 2.723 B3L CE2 CD CG 108.95 2.259 B3L CE1 CD CG 110.95 2.656 B3L H1E2 CE2 H2E2 105.67 2.934 B3L H2E2 CE2 H3E2 105.78 2.934 B3L H1E2 CE2 H3E2 107.05 2.933 B3L H2E2 CE2 CD 112.73 2.662 B3L H3E2 CE2 CD 111.91 2.665 B3L H1E2 CE2 CD 113.17 2.686 B3L H1E1 CE1 H2E1 106.00 2.935 B3L H2E1 CE1 H3E1 106.10 2.936 B3L H1E1 CE1 H3E1 105.73 2.935 B3L H2E1 CE1 CD 113.07 2.437 B3L H3E1 CE1 CD 112.17 2.708 B3L H1E1 CE1 CD 113.17 2.649 # loop_ _chem_comp_tor.comp_id _chem_comp_tor.id _chem_comp_tor.atom_id_1 _chem_comp_tor.atom_id_2 _chem_comp_tor.atom_id_3 _chem_comp_tor.atom_id_4 _chem_comp_tor.value_angle _chem_comp_tor.value_angle_esd _chem_comp_tor.period B3L Var_01 CB CA C O 54.55 30.0 2 B3L Var_02 CE1 CD CG CB -66.07 30.0 1 B3L Var_03 H1E1 CE1 CD CG -19.34 30.0 3 B3L Var_04 H1E2 CE2 CD CG 93.46 30.0 3 # loop_ _chem_comp_chir.comp_id _chem_comp_chir.id _chem_comp_chir.atom_id_centre _chem_comp_chir.atom_id_1 _chem_comp_chir.atom_id_2 _chem_comp_chir.atom_id_3 _chem_comp_chir.volume_sign B3L chir_01 CB CA N CG negativ # loop_ _chem_comp_plane_atom.comp_id _chem_comp_plane_atom.plane_id _chem_comp_plane_atom.atom_id _chem_comp_plane_atom.dist_esd B3L plan-1 O 0.020 B3L plan-1 C 0.020 B3L plan-1 CA 0.020 B3L plan-1 OXT 0.020

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phenix.model_idealization
by Manoj saxena 21 Jun '23

21 Jun '23

Hi , I am trying to fix a pdb file that was obtained from Rosetta and has some distorted helices so I trier to fix that with > phenix.model_idealization model.pdb use_ss_restraints = True I am attaching the log file , here is the end of the log file. Any suggestions on what's going on ? " NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Traceback (most recent call last): File "/Applications/phenix-1.20.1-4487/build/../modules/cctbx_project/mmtbx/command_line/model_idealization.py", line 1118, in <module> run(sys.argv[1:]) File "/Applications/phenix-1.20.1-4487/build/../modules/cctbx_project/mmtbx/command_line/model_idealization.py", line 1106, in run mi_object.run() File "/Applications/phenix-1.20.1-4487/build/../modules/cctbx_project/mmtbx/command_line/model_idealization.py", line 548, in run self._setup_model_h() File "/Applications/phenix-1.20.1-4487/build/../modules/cctbx_project/mmtbx/command_line/model_idealization.py", line 478, in _setup_model_h params_h.pdb_interpretation = self.model._pdb_interpretation_params.pdb_interpretation AttributeError: 'NoneType' object has no attribute 'pdb_interpretation'" My aim is to idealize the secondary structure. I first tried it in Isolde but the EM density is not great and always leads to some distortion. So I was wondering if I can do this fix in Phenix. Is this model idealization tool the best approach? or I have to go in and fix things manually. Thanks Manoj

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