- phenixbb - phenix-online.org

Trouble with GTP/GDP refinement.
by DIEGO ORTIZ DE ELGUEA LOPEZ DE DICASTILLO 18 Mar '25

18 Mar '25

Dear phenixbb: I'm working with a GTP binding protein and have had some problems running phenix_refine. In my unit cell there are two molecules one with GDP and one with GTP, which I added in Coot(0.9.8). When refining the following error message pops-up : "Fatal problems interpreting model file: Number of atoms with unknown nonbonded energy type symbols:4 Please edit the model file to resolve the problems and/or supply a CIF file with matching restraint definitions, along with apply_cif_modifications and apply_cif_link parameter definitions if necessary". Checking the log file I found that the problem seems to be hydrogen atoms from these ligands Number of atoms with unknown nonbonded energy type symbols: 4 "HETATM 6499 H5' GTP A 501 .*. H " "HETATM 6502 H5'' GTP A 501 .*. H " "HETATM12939 H5' GDP B 501 .*. H " "HETATM12940 H5'' GDP B 501 .*. H " Including the corresponding .CIF files (dowloaded from PDB) did not solve the problem and the same error popped. Since I'm in the initial stages of the refinement I'm running phenix with bindividuals. Could anybody save my day giving me some light into this issue? Cheers, Diego

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.cif file has 'UNK' auth_asym_id
by Kevin M Jude 14 Mar '25

14 Mar '25

I’ve finished refining a structure with three protein chains A, B, C. The pdb file looks ‘normal’ to me, but when I inspect the .cif file written by phenix, the auth_asym_id for chains B and C is ‘UNK’. label_asym_id is correct for all chains. I’m not really sure what the difference is between the auth_ and label_ fields. When I try to perform actions on the .cif file, I get duplicate atom label errors. Here’s a few example lines from the .pdb and .cif files, where auth_asym_id is field 6 and label_asym_id is field 16 ATOM 460 OXT PRO A 59 5.272 55.689 31.481 1.00 52.63 O ANISOU 460 OXT PRO A 59 6541 6212 7244 1448 1260 96 O TER ATOM 461 N ALA B 2 39.292 61.974 39.403 1.00 67.81 N ANISOU 461 N ALA B 2 7118 8729 9916 -1711 -388 2066 N ATOM 460 OXT . PRO A 59 ? 5.27169 55.68852 31.48123 1.000 52.63052 O ? A ? 58 1 ATOM 461 N . ALA UNK 2 ? 39.29207 61.97430 39.40271 1.000 67.80544 N ? B ? 1 1 I’m able to convert the pdb file to a usable cif file using gemmi but wanted to report this weird behavior with phenix 1.21.2_5419. -- 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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Pdb validation report via phenix
by Stachowski, Tim 12 Mar '25

12 Mar '25

I’ve always found the phenix.get_pdb_validation tool to be super helpful to gauge where my refinements are relative to the PDB, especially since I work mainly through the command line. But sometime around late last year, the R-free metric stopped being calculated (probably related to “EDS: FAILED”). Is there a way to bring this part of the tool back – or does anyone have a work around they can share? I’m running the command like: phenix.get_pdb_validation_report final-coot-3_refine_001.reflections.cif final-coot-3_refine_001.cif with version: phenix-2.0rc1-5599 Thanks Tim -- Tim Stachowski, PhD St. Jude Children’s Research Hospital ________________________________ Email Disclaimer: www.stjude.org/emaildisclaimer Consultation Disclaimer: www.stjude.org/consultationdisclaimer

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Refining the structure of Ribosome and the system crash
by Rajnandani Kashyap 12 Mar '25

12 Mar '25

Hello Everyone I am trying to run jobs in phenix (real space refinement alignment with the other modelling jobs), but the system always crashes, and refinement doesn't complete. This is the structure of ribosome, and I am wondering what to do to get through the refinement. Is there any specific parameters I should be using. I tried to change the processors to 15 for a 20-processor computer. Let me know. Thanks in advance. FYI: There is no error message in the log. Best, Rajnandani ---------------------------------------------------------------------- Rajnandani Kashyap, Ph.D. Postdoctoral Fellow Department of Biochemistry and Molecular Biology Saint Louis University, Antony Lab 1205 Carr Lane, DRC 451 St. Louis, MO 63104 https://orcid.org/0000-0002-9141-1168 -----------------------------------------------------------------------

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Ion placement (anomalous) + occupancy refinement
by miha.pavsic＠fkkt.uni-lj.si 06 Mar '25

06 Mar '25

Hi everyone, I have a dataset from a protein that contains 2 Ca2+ binding sites. The Ca2+ loaded protein was crystallized in the presence of Tb3+ which at one site mostly replaced Ca2+, however at the other site the Tb3+/Ca2+ ratio appears to be much lower (judging from anomalous map; data collected at 1.3 Å wavelength, MR for phasing). The occupancy sum of Tb3+ and Ca2+ at each of the two sites is strongly believed to be 1. While I am aware of the ion placement option in phenix.refine, I am not so sure how to refine the partial occupancies using anomalous data, if possible. Many thanks for any hints, Miha

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AKM in Phenix
by lucas.santosouza＠outlook.com 06 Mar '25

06 Mar '25

Hi everyone, Is there still support for the generation of Average Kick Maps in Phenix? I am using both versions 1.21.2-5419 and the nightly build 2.0rc1-5555. I added kicked=True to the maps.params, but phenix.maps gives me "Unused parameter definitions: maps.map_coefficients.kicked (file "maps.params", line 53)". I also cannot see the "Kicked map" check box in the Create Maps GUI. Cheers, Lucas

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Refine partially occupied ligand in active site containing chloride ions
by Stephen.carr＠rc-harwell.ac.uk 06 Mar '25

06 Mar '25

Dear phenix bb, I am trying to refine a ligand in the active site of my protein where the ligand occupancy is ~50%. The empty active site contains two chloride ions and the residual density from these ions is very prominent when the model is refined with the ligand alone. I would like to refine the model with both the ligand and chloride ions present and have been trying to do this with altLoc flags but so far with no luck. I'm assuming that since the Cl ions more-or-less directly overlay atoms from the ligand positional refinement keeps pushing them out of the density. I'm sure there is a simple way to get around this and I would be grateful for any suggestions. Best wishes, Steve Dr Stephen Carr Research Complex at Harwell (RCaH) Rutherford Appleton Laboratory Harwell Oxford Didcot Oxon OX11 0FA United Kingdom Email stephen.carr(a)rc-harwell.ac.uk tel 01235 567717 This email and any attachments may contain confidential, copyright and or privileged material, and are for the use of the intended addressee only. If you are not the intended addressee or an authorized recipient of the addressee, please notify us of receipt by returning the e-mail and do not use, copy, retain, distribute or disclose the information in or attached to this email. Any views or opinions presented are solely those of the author and do not necessarily represent those of the Research Complex at Harwell. There is no guarantee that this email or any attachments are free from viruses and we cannot accept liability for any damage which you may sustain as a result of software viruses which may be transmitted in or with the message. We use an electronic filing system. Please send electronic versions of documents, unless paper is specifically requested. This email may have a protective marking, for an explanation, please see: http://www.mrc.ac.uk/About/informationandstandards/documentmarking/index.htm.

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Program crash
by F.Xavier Gomis-Rüth 05 Mar '25

05 Mar '25

Dear all, I recently upgraded my MacOS to Sequoia 15.3.1 and found that previous phenix jobs that ran without problem suddenly crashed with the installation (phenix-1-21.2-5419) I had since August 2024. So I installed the latest on-built (phenix-2.0rc-5617) but it nonetheless crashed with the message below. Any help would be greatly appreciated. Best, Xavier XGRMAC:cyc3 > Could not import the compiled Python-sander interface.Traceback (most recent call last): File "/Applications/phenix-2.0rc1-5617/lib/python3.9/site-packages/phenix/command_line/real_space_refine.py", line 8, in <module> run_program(real_space_refine.Program) File "/Applications/phenix-2.0rc1-5617/lib/python3.9/site-packages/iotbx/cli_parser.py", line 980, in run_program task.run() File "/Applications/phenix-2.0rc1-5617/lib/python3.9/site-packages/phenix/programs/real_space_refine.py", line 206, in run self.rsr_result = rsr_wrappers.run_real_space_refine( File "/Applications/phenix-2.0rc1-5617/lib/python3.9/site-packages/phenix/refinement/rsr/wrappers.py", line 52, in __init__ self._refined = macro_cycle_real_space.run( File "/Applications/phenix-2.0rc1-5617/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/Applications/phenix-2.0rc1-5617/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/Applications/phenix-2.0rc1-5617/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 704, in refine_xyz self.minimization_ncs() File "/Applications/phenix-2.0rc1-5617/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 794, in minimization_ncs weight = real_space_weight.run( File "/Applications/phenix-2.0rc1-5617/lib/python3.9/site-packages/mmtbx/refinement/real_space/weight.py", line 84, in __init__ ro.refine( File "/Applications/phenix-2.0rc1-5617/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 394, in refine real_space_result = refinery( File "/Applications/phenix-2.0rc1-5617/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 233, in __init__ refiner.refine( File "/Applications/phenix-2.0rc1-5617/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 126, in refine minimized = mmtbx.refinement.minimization_ncs_constraints.lbfgs( File "/Applications/phenix-2.0rc1-5617/lib/python3.9/site-packages/mmtbx/refinement/minimization_ncs_constraints.py", line 424, in __init__ minimizer = scitbx.lbfgs.run( File "/Applications/phenix-2.0rc1-5617/lib/python3.9/site-packages/scitbx/lbfgs/__init__.py", line 270, in run return run_c_plus_plus( File "/Applications/phenix-2.0rc1-5617/lib/python3.9/site-packages/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/Applications/phenix-2.0rc1-5617/lib/python3.9/site-packages/mmtbx/refinement/minimization_ncs_constraints.py", line 456, in compute_functional_and_gradients t,g = self.target_and_grads_object.target_and_gradients( File "/Applications/phenix-2.0rc1-5617/lib/python3.9/site-packages/mmtbx/refinement/minimization_ncs_constraints.py", line 242, in target_and_gradients t_restraints, g_restraints = restraints_target_and_grads( File "/Applications/phenix-2.0rc1-5617/lib/python3.9/site-packages/mmtbx/refinement/minimization_ncs_constraints.py", line 110, in restraints_target_and_grads ef = restraints_manager.energies_sites( File "/Applications/phenix-2.0rc1-5617/lib/python3.9/site-packages/cctbx/geometry_restraints/manager.py", line 1524, in energies_sites pair_proxies = self.pair_proxies( File "/Applications/phenix-2.0rc1-5617/lib/python3.9/site-packages/cctbx/geometry_restraints/manager.py", line 1427, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/Applications/phenix-2.0rc1-5617/lib/python3.9/site-packages/cctbx/geometry_restraints/manager.py", line 1308, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 59.7151 > 50: distance: 0 - 1: 15.382 distance: 1 - 2: 14.133 distance: 1 - 3: 15.077 distance: 4 - 5: 11.010 distance: 5 - 6: 5.064 distance: 5 - 8: 12.166 distance: 6 - 7: 9.252 distance: 6 - 15: 4.656 distance: 8 - 9: 6.568 distance: 9 - 10: 41.112 distance: 9 - 11: 19.959 distance: 10 - 12: 4.365 distance: 11 - 13: 12.611 distance: 12 - 14: 28.654 distance: 13 - 14: 25.314 distance: 15 - 16: 7.291 distance: 16 - 17: 12.341 distance: 16 - 19: 4.354 distance: 17 - 18: 11.820 distance: 17 - 26: 9.661 distance: 19 - 20: 7.438 distance: 20 - 21: 17.074 distance: 20 - 22: 19.126 distance: 21 - 23: 7.637 distance: 22 - 24: 3.434 distance: 23 - 25: 24.169 distance: 24 - 25: 8.875 distance: 26 - 27: 10.037 distance: 27 - 28: 9.377 distance: 27 - 30: 12.844 distance: 28 - 29: 12.437 distance: 28 - 34: 22.926 distance: 30 - 31: 46.409 distance: 31 - 32: 6.849 distance: 31 - 33: 21.459 distance: 34 - 35: 12.375 distance: 34 - 40: 15.635 distance: 35 - 36: 10.511 distance: 35 - 38: 12.461 distance: 36 - 37: 11.525 distance: 36 - 41: 15.668 distance: 38 - 39: 9.083 distance: 39 - 40: 10.922 distance: 41 - 42: 15.925 distance: 42 - 43: 26.537 distance: 42 - 45: 20.600 distance: 43 - 44: 14.038 distance: 43 - 48: 40.043 distance: 45 - 46: 18.721 distance: 45 - 47: 12.152 distance: 48 - 49: 19.936 distance: 49 - 50: 9.210 distance: 49 - 52: 4.170 distance: 50 - 51: 6.051 distance: 50 - 56: 10.707 distance: 52 - 53: 13.486 distance: 53 - 54: 25.122 distance: 53 - 55: 30.977 distance: 56 - 57: 24.676 distance: 57 - 58: 6.469 distance: 57 - 60: 24.810 distance: 58 - 59: 19.649 distance: 58 - 65: 16.713 distance: 60 - 61: 19.749 distance: 61 - 62: 27.563 distance: 62 - 63: 31.258 distance: 63 - 64: 39.081 distance: 65 - 66: 17.034 distance: 66 - 67: 13.877 distance: 66 - 69: 30.087 distance: 67 - 68: 30.739 distance: 67 - 70: 22.852 distance: 70 - 71: 17.537 distance: 71 - 72: 19.009 distance: 71 - 74: 23.249 distance: 72 - 73: 32.627 distance: 72 - 81: 23.614 distance: 74 - 75: 30.150 distance: 75 - 76: 11.440 distance: 75 - 77: 13.841 distance: 76 - 78: 23.906 distance: 77 - 79: 27.669 distance: 78 - 80: 29.196 distance: 79 - 80: 27.009 --

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Cryo_fit installation
by omar.debei＠unipr.it 28 Feb '25

28 Feb '25

Hi everyone, I was wondering if you could help me with installing cryo_fit on an Ubuntu machine. I followed the instructions here for the cryo_fit installation. Then, I tried to follow this guide to install gromacs_cryo_fit. However, I got stuck at the "Install using a provided script" step. Do I need to install GROMACS separately before proceeding? Any tips would be greatly appreciated! Many thanks, Omar

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Register by Feb. 28th for the West Coast Structural Biology Workshop
by Michael Thompson 21 Feb '25

21 Feb '25

The registration and abstract submission deadlines for the 26th West Coast Structural Biology Workshop are just one week away... Register today, and be a part of this iconic meeting with over 50 years of tradition!! See below for a message about the conference: Dear Colleagues, The registration and abstract submission deadlines for the upcoming West Coast Structural Biology Workshop have been extended! The UPDATED deadlines for registration and abstract submission are Feb. 28, 2025. The meeting is scheduled for March 23-26, 2025 at its traditional location, the Asilomar Conference Center in Pacific Grove, CA. The conference website can be found at: https://wcsbw2025.macromolecules.xyz/. The WCSBW is a bi-annual meeting that showcases the latest methods, developments, and discoveries in structural biology, including X-ray Crystallography, Cryo-EM, NMR, and other methods. We strongly encourage anyone interested in method development and solutions to technical challenges in structural analysis to attend, even if you're not from the west coast. Importantly, the WCSBW aims to highlight the work of trainees, so all oral presentations (except keynotes) will be given by students and postdocs. The 26th edition of this meeting will include: * Opportunities to connect with leaders in the field, exchange practical advice, and stay at the forefront of structural biology advancements. * Exciting oral research presentations and engaging poster sessions. * Inspiring keynote presentations, featuring Prof. Bil Clemons from Caltech, and Dr. Junko Yano from Lawrence Berkeley National Lab. * A 2-hour workshop hosted by the Phenix developers, detailing the use of new tools for structure determination and analysis. * A networking session with scientists from west coast biotech companies for students and postdocs who are entering the job market. * Good company and beautiful views of the pacific ocean! Some details about the conference are included below, and more information is available at our website (see link above). We hope to see you at Asilomar in March! -Mike Thompson (UC Merced) and Alec Follmer (UC Davis) P.S. We ask for your help in sharing this announcement with any students, postdocs, staff, colleagues, collaborators, or friends that might be interested. Thanks! Conference Details: March 23-26, 2025 at Asilomar Conference Center in Pacific Grove, CA Visit the conference website at: https://wcsbw2025.macromolecules.xyz/ Registration: https://book.passkey.com/event/50870517/owner/10793795/home Registration fee is $200, plus lodging fees (meals included). Attendees need to book their lodging accommodations at Asilomar when registering for the conference. Both single and double occupancy rooms are available. If you do not have a roommate and would like us to pair you with one to lower costs, or if you would like to register for the conference and arrange your own accommodations offsite, please contact us at wcsbw2025(a)gmail.com<mailto:[email protected]>. Abstract Submission: https://wcsbw2025.macromolecules.xyz/registration/ All oral presentations at the WCSBW, except for the keynotes, will be given by trainees. Students (undergraduate or graduate) and Postdocs are welcome to submit abstracts for oral presentations. We welcome abstracts for poster presentations from attendees at any career stage. The deadline for submitting abstracts is February 28, 2025, and attendees must be registered for the meeting in order for their abstracts to be considered. Abstracts that are submitted for oral presentations and not selected will be automatically considered as poster abstracts. --- Michael C. Thompson, Ph.D. (he/him) Assistant Professor Dept. of Chemistry and Biochemistry University of California, Merced https://thompsonlab.science<https://urldefense.com/v3/__https://thompsonlab.science__;!!LQC6Cpwp!-fv-nQ…>

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Postdoc and PhD positions in quantum/protein/electron crystallography. Application deadline March 2nd
by Paulina Dominiak 03 Feb '25

03 Feb '25

Dear Colleagues, We currently have several positions available in my group at the University of Warsaw - both postdoc and PhD. The research project combines quantum crystallography with protein crystallography, focusing on 3DED/microED techniques. We're interested in hearing from researchers with different backgrounds: * Software developers who want to learn crystallography * Protein crystallographers looking to expand their skills * Small-molecule crystallographers experienced with X-ray charge density studies * Researchers familiar with electron crystallography Detailed information about the positions, project description, and application links can be found at: http://4xeden.uw.edu.pl/2025/01/18/bio-qcr/ <http://4xeden.uw.edu.pl/2025/01/18/bio-qcr/> Application deadline: March 2nd, 2025 Please share this opportunity with qualified candidates who might be interested. For additional information, feel free to contact me directly. Best regards, Paulina -- Prof. dr hab. Paulina M. Dominiak Group Leader Electron Density Modelling Group Laboratory for Structural and Biochemical Research (LBSBio) Biological and Chemical Research Centre Department of Chemistry University of Warsaw ul. Zwirki i Wigury 101 02-089 Warszawa, Poland Room: 3.125 E-mail:[email protected] Phone: (48) 22 55 26 714 WWW:http://4xeden.uw.edu.pl

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DEADLINE EXTENDED: 26th West Coast Structural Biology Workshop
by Michael Thompson 03 Feb '25

03 Feb '25

Dear Colleagues, The registration and abstract submission deadlines for the upcoming West Coast Structural Biology Workshop have been extended! The UPDATED deadlines for registration and abstract submission are Feb. 28, 2025 and Feb. 21, 2025 respectively. The meeting is scheduled for March 23-26, 2025 at its traditional location, the Asilomar Conference Center in Pacific Grove, CA. The conference website can be found at: https://wcsbw2025.macromolecules.xyz/. The WCSBW is a bi-annual meeting that showcases the latest methods, developments, and discoveries in structural biology, including X-ray Crystallography, Cryo-EM, NMR, and other methods. We strongly encourage anyone interested in method development and solutions to technical challenges in structural analysis to attend, even if you're not from the west coast. Importantly, the WCSBW aims to highlight the work of trainees, so all oral presentations (except keynotes) will be given by students and postdocs. The 26th edition of this meeting will include: * Opportunities to connect with leaders in the field, exchange practical advice, and stay at the forefront of structural biology advancements. * Exciting oral research presentations and engaging poster sessions. * Inspiring keynote presentations, featuring Prof. Bil Clemons from Caltech, and Dr. Junko Yano from Lawrence Berkeley National Lab. * A 2-hour workshop hosted by the Phenix developers, detailing the use of new tools for structure determination and analysis. * A networking session with scientists from west coast biotech companies for students and postdocs who are entering the job market. * Good company and beautiful views of the pacific ocean! Some details about the conference are included below, and more information is available at our website (see link above). We hope to see you at Asilomar in March! -Mike Thompson (UC Merced) and Alec Follmer (UC Davis) P.S. We ask for your help in sharing this announcement with any students, postdocs, staff, colleagues, collaborators, or friends that might be interested. Thanks! Conference Details: March 23-26, 2025 at Asilomar Conference Center in Pacific Grove, CA Visit the conference website at: https://wcsbw2025.macromolecules.xyz/ Registration: https://book.passkey.com/event/50870517/owner/10793795/home Registration fee is $200, plus lodging fees (meals included). Attendees need to book their lodging accommodations at Asilomar when registering for the conference. Both single and double occupancy rooms are available. If you do not have a roommate and would like us to pair you with one to lower costs, or if you would like to register for the conference and arrange your own accommodations offsite, please contact us at wcsbw2025(a)gmail.com<mailto:[email protected]>. Abstract Submission: https://wcsbw2025.macromolecules.xyz/registration/ All oral presentations at the WCSBW, except for the keynotes, will be given by trainees. Students (undergraduate or graduate) and Postdocs are welcome to submit abstracts for oral presentations. We welcome abstracts for poster presentations from attendees at any career stage. The deadline for submitting abstracts is February 21, 2025, and attendees must be registered for the meeting in order for their abstracts to be considered. Abstracts that are submitted for oral presentations and not selected will be automatically considered as poster abstracts. --- Michael C. Thompson, Ph.D. (he/him) Assistant Professor Dept. of Chemistry and Biochemistry University of California, Merced https://thompsonlab.science<https://urldefense.com/v3/__https://thompsonlab.science__;!!LQC6Cpwp!-fv-nQ…>

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Re: Uknown non bonded
by Yann Lefrançois.C 30 Jan '25

30 Jan '25

Hi thank you for your reply, I'm not working with ligand, but a complexe. I do not have hydrogen in my model, so it seems I have a bigger problem. [image: image.png] I tried to use PDB_REDO, however i'm using mrc format for my ED map Le jeu. 30 janv. 2025 à 16:39, Georg Mlynek <georg.mlynek(a)univie.ac.at> a écrit : > Hi Yann, can you post a screenshot of the error message? It should be > stated there which are causing problems. > > Very often the problems are hydrogens. So just delete those. One easy > way is to do is to open in coot and when saving there is a tick box > without hydrogens. There are also tools in phenix doing this. > > Also you can submit the pdb to PDB_REDO to check if there are more sever > problems. If PDB_REDO runs then there are no big errors. Then just use > the output for phenix refine. > > And as Xavier wrote ligands also can cause problems. But also there most > times the hydrogens. > > Br, Georg. > > > Am 2025-01-30 um 4:26 PM schrieb yannlefrancoiscopy(a)gmail.com: > > Hello, > > I'm a newbie phenix user, and i was trying to refine a model. > > > > and when i tried to refine it, I got an error message saying that some > atoms had unknown nonbonded interaction. > > > > However, there are no indication to which one are problematic, Any tips > on how to find the problematic one and how to correct them ? > > > > best wishes, > > Yann > > _______________________________________________ > > 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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Uknown non bonded
by yannlefrancoiscopy＠gmail.com 30 Jan '25

30 Jan '25

Hello, I'm a newbie phenix user, and i was trying to refine a model. and when i tried to refine it, I got an error message saying that some atoms had unknown nonbonded interaction. However, there are no indication to which one are problematic, Any tips on how to find the problematic one and how to correct them ? best wishes, Yann

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open position for a 2(+2) year postdoc working on plant sugar and hormone transport at Aarhus University, Denmark.
by Bjørn Panyella Pedersen 29 Jan '25

29 Jan '25

Dear colleagues, Please pass this along anyone who might be interested. Thanks! /Bjørn Postdoctoral position in biophysical and structural characterization of sugar and hormone transport, Denmark online posting: https://international.au.dk/about/profile/vacant-positions/job/postdoctoral… We are looking for a highly skilled and motivated postdoc with an interest in working on sugar and hormone transporting membrane transporters and preferably with a proven track record in the area of structural and/or functional analysis of membrane proteins. The position will be open from spring 2025, but starting date is negotiable. Funding is available for at least 2 years of employment, with an extension possible for up to a total of 4 years. The position: The position seeks to strengthen ongoing activities in the our group related to the function and mechanism of sugar and hormone-transporting membrane proteins in plants (pedersenlab.dk). Examples of our research can be found in: Schulz & Ung et al. "Transport of herbicides by PIN-FORMED auxin transporters" bioRxiv (2024) Andersen et al. Basis of Glucose and Fructose Selectivity in Sugar Transport Proteins" bioRxiv (2024) Bavnhøj et al. “Structure and sucrose binding mechanism of the plant SUC1 sucrose transporter.” Nature Plants 7 (2023) Ung et al. “Structures and mechanism of the plant PIN-FORMED auxin transporter” Nature 609 (2022). The laboratory's interest is the interplay between structure and function of transmembrane transport processes with a focus on metabolite uptake systems and proton driven transport, and the methods uses are primarily structural biology (cryo-EM, crystallography) and biochemistry. The group is part of the Section of Structural Biology at Aarhus University. The candidate: A successful candidate has a relevant Ph.D. degree and a solid and documented background in structural biology, biochemistry and/or biophysics. Experience with membrane protein expression and purification is favored, and the candidate must demonstrate an ability and interest to work with membrane proteins with a structural aim. Applicants should be ambitious, show strong collaborative skills, and be able to take initiatives and responsibility within the work environment. The successful candidate is offered: - access to a well-developed research infrastructure. - an exciting interdisciplinary environment with many national, international and industrial collaborators. - a research climate inviting lively, open and critical discussion within and across different fields of research. - a working environment with teamwork, close working relations, network activities among young scientists and social activities. - a workplace characterized by professionalism, equality and a healthy work-life balance. The city: In Aarhus you have easy access to beautiful nature, an exciting culture and city life as well as a safe environment for children - a great place for the whole family. The city of Aarhus has everything you need: exciting national and international jobs, delightful residential areas, a rich cultural life, and beautiful surrounding landscape of woods and coastline that make Aarhus a wonderful place to live and work. See “life in Denmark” at Aarhus and surroundings for further details on the city and the university (https://international.au.dk/life/locations/aarhusandsurroundings). Deadline: All applications must be made online and received by 28. Feb. 2025 using the online application system (link above).

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Reminder: Phenix Postdoc Position - Berkeley, California
by Paul Adams 27 Jan '25

27 Jan '25

Dear Colleagues, The Phenix team is hiring! We are looking for talented postdoctoral candidates to join the group in Berkeley. Please see the details below, and feel free to pass on to anyone you think might be interested. To access the job posting directly: https://jobs.lbl.gov/jobs/computational-postdoctoral-fellow-6893 Cheers, Paul Berkeley Lab’s (LBNL) Molecular Biophysics and Integrated Bioimaging Division (MBIB) has an opening for a Postdoctoral Fellow to develop new computational methods for the structure determination and refinement of protein structures using the PHENIX software system. In this exciting role, you will work under the direction of the Deputy Director for this project with primary responsibilities including the development and implementation of numerical methods and new computational protocols, including the application of machine learning methods. The goals of the role include the development of automated pipelines for data analysis, structure completion and model validation. The Phenix software is used worldwide for the determination of atomic structures using X-ray and neutron crystallography and cryo-electron microscopy. The software is developed as part of an international collaboration supported by the National Institutes of Health and the Phenix Industrial Consortium. This will require the organization of results for presentation and viewing by project team members, the wider scientific community, and preparing results for publication in scientific journals. This position has an earliest start date of February 3, 2025. What You Will Do: Develop and implement computational algorithms for structure determination using crystallography and cryo-electron microscopy including: Improved methods for the optimization and completion of models Automated pipelines for data analysis, structure completion, and model validation Apply machine learning methods to problems in crystallography and cryo-electron microscopy. Develop and test new components of the PHENIX software system in collaboration with others. Document software developments. Collaborate with other researchers in the PHENIX program. Summarize research results, publish them in peer-reviewed journals, and contribute to scientific research papers and reports. Contribute to discussions on the determination of future directions. Attend group meetings or conferences/workshops, present status reports, and scientific findings as appropriate. Keep accurate and detailed research notes. What is Required: A recent Ph.D. (within the last 1-2 years) in Computational Crystallography, Computational Cryo-Electron Microscopy, Computational Biology, Bioinformatics, Computational Chemistry or a closely related field. Demonstrated experience in developing computational algorithms for solving problems. Demonstrated experience with computational methods development. Publications in macromolecular crystallography, cryo-electron microscopy or closely related fields. Good programming and mathematical skills, including familiarity with Python and other software development tools. Strong organizational skills including experience maintaining detailed and accurate records of experiment results and analyzed data. Excellent oral and written communication skills including experience organizing/presenting technical reports. Demonstrated interpersonal skills including experience conducting experiments independently and collaborating with a diverse interdisciplinary research team. Desired Qualifications: Experience with machine learning methods, programming with C++, or equivalent object-oriented programming languages. Experience with the practical aspects of crystallography and/or cryo-electron microscopy. Familiarity with macromolecular structure or computational chemistry. -- 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 [ MEEspinosa(a)lbl.gov ][ 1-510-333-6788 ] Phenix Consortium: Ashley Dawn [ AshleyDawn(a)lbl.gov ][ 1-510-486-5455 ] --

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About d99
by Roberto Battistutta 24 Jan '25

24 Jan '25

Dear Phenix people, In "New tools for the analysis and validation of cryo-EM maps and atomic models” (ActaD 2018), it is reported that "map sharpening can affect d99 (Fig. 9g) but it is rather insensitive to masking (Fig. 9h).” I have a case where d99 increases a lot with masking, as shown in the screenshot below (from Mtriage). On the other hand, FSC decreases. What does this mean? Can it be attributed to the fact that there is a strong scatterer in the molecule (a heavy atom) that strongly influences the intensity of the map? Are there other possible explanations (preferential orientation for example)? What is the best way to handle such maps? Thank you for the attention. Best, Roberto. Roberto Battistutta Associate Professor Department of Chemical Sciences University of Padua via Marzolo 1, 35131 Padova - ITALY tel. +39.049.827.5262 fax. +39.049.827.5829 roberto.battistutta(a)unipd.it

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André Mitschler, former crystallography engineer in the BSI department, Strasbourg
by Alexandre OURJOUMTSEV 24 Jan '25

24 Jan '25

Sorry, my previous e-mail left with a wrong subject… Sacha = = = = Dear all, for those (I expect, many of you) who knew André Mitschler, I resubmit the message below. Sad news. It was a great and non-trivial person. With best wishes, Sacha Urzhumtsev = = = = From: Valerie LAMOUR <lamourv(a)igbmc.fr<mailto:[email protected]>> Sent: Friday, January 24, 2025 4:23 PM Subject: André Mitschler, former crystallography engineer in the BSI department André Mitschler est décédé le 5 Décembre, à l’âge de 83 ans. André était un cristallographe expérimental hors pair. Il a débuté en recherche dans le laboratoire du Prof Weiss où il a eu la charge du premier diffractomètre à RX de l’époque. En 1967, a entamé une fructueuse collaboration avec Dino Moras qui a pu bénéficier de son expertise et son adresse expérimentale pour sa thèse de 3e cycle. Leurs liens ne se sont jamais rompus. En 1981 Il a rejoint le laboratoire de cristallographie de Dino, nouvellement créé à l’IBMC. Il y a effectué le reste d’une fructueuse carrière d’ingénieur CNRS qui, en 1994, s’est poursuivie à l’IGBMC, un nouvel institut créé à Illkirch avec un important soutien de l’industrie pharmaceutique. En 1996, il a rejoint le groupe d’Alberto Podjarny, pour travailler dans la détermination de la structure de l’Aldose Reductase humaine. Les cristaux diffractaient à une résolution extrêmement haute (0.6 Angstroms). La mesure des données a demandé des nouveaux développements et l’utilisation des meilleures lignes synchrotron du monde. André était à la hauteur du défi, avec la capacité de passer de longues heures à monter et tester expérimentalement des cristaux. Il pouvait travailler 72 heures d’affilée dans le synchrotron d'Argonne National Lab. Le travail a culminé en 2008, avec la publication d’un mécanisme enzymatique inattendu. En 1999, il a obtenu la médaille de Cristal du CNRS, en reconnaissance de ses travaux en cristallographie expérimentale. André était aussi un passionné de l’histoire militaire, et a fait une carrière dans l’armée jusqu’à rang de colonel dans la cavalerie. Sa passion par la recherche, sa force de travail et son dévouement pour l’excellence expérimentale sont un exemple à suivre par tous les jeunes chercheurs. //// André Mitschler passed away on December 5th at the age of 83. André was an outstanding experimental crystallographer. He began his research career in Professor Weiss's laboratory, where he was responsible for the first X-ray diffractometer at the time. In 1967, he started a fruitful collaboration with Dino Moras, whose doctoral work benefited greatly from André's expertise and experimental skill. Their professional ties endured throughout their lives. In 1981, André joined Dino’s newly established crystallography laboratory at IBMC, where he spent the remainder of a productive career as a CNRS engineer. In 1994, he continued his work at IGBMC, a new institute in Illkirch supported by the pharmaceutical industry. In 1996, André joined Alberto Podjarny’s group to work on determining the structure of human aldose reductase. The crystals diffracted at an exceptionally high resolution (0.6 Å), which required innovative developments and access to the world's most advanced synchrotron beamlines. André rose to the challenge, demonstrating his ability to spend long hours preparing and experimentally testing crystals. He worked tirelessly, including 72-hour shifts at the Argonne National Laboratory synchrotron. This effort culminated in 2008 with the publication of an unexpected enzymatic mechanism. In 1999, André was awarded the CNRS Crystal Medal in recognition of his contributions to experimental crystallography. André was also a military history enthusiast and pursued a parallel career in the army, rising to the rank of colonel in the cavalry. His passion for research, tireless work ethic, and dedication to experimental excellence remain an inspiration for young researchers.

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Phenix Postdoc Position - Berkeley, California
by Paul Adams 24 Jan '25

24 Jan '25

Dear Colleagues, The Phenix team is hiring! We are looking for talented postdoctoral candidates to join the group in Berkeley. Please see the details below, and feel free to pass on to anyone you think might be interested. To access the job posting directly: https://jobs.lbl.gov/jobs/computational-postdoctoral-fellow-6893 Cheers, Paul Berkeley Lab’s (LBNL) Molecular Biophysics and Integrated Bioimaging Division (MBIB) has an opening for a Postdoctoral Fellow to develop new computational methods for the structure determination and refinement of protein structures using the PHENIX software system. In this exciting role, you will work under the direction of the Deputy Director for this project with primary responsibilities including the development and implementation of numerical methods and new computational protocols, including the application of machine learning methods. The goals of the role include the development of automated pipelines for data analysis, structure completion and model validation. The Phenix software is used worldwide for the determination of atomic structures using X-ray and neutron crystallography and cryo-electron microscopy. The software is developed as part of an international collaboration supported by the National Institutes of Health and the Phenix Industrial Consortium. This will require the organization of results for presentation and viewing by project team members, the wider scientific community, and preparing results for publication in scientific journals. This position has an earliest start date of February 3, 2025. What You Will Do: Develop and implement computational algorithms for structure determination using crystallography and cryo-electron microscopy including: Improved methods for the optimization and completion of models Automated pipelines for data analysis, structure completion, and model validation Apply machine learning methods to problems in crystallography and cryo-electron microscopy. Develop and test new components of the PHENIX software system in collaboration with others. Document software developments. Collaborate with other researchers in the PHENIX program. Summarize research results, publish them in peer-reviewed journals, and contribute to scientific research papers and reports. Contribute to discussions on the determination of future directions. Attend group meetings or conferences/workshops, present status reports, and scientific findings as appropriate. Keep accurate and detailed research notes. What is Required: A recent Ph.D. (within the last 1-2 years) in Computational Crystallography, Computational Cryo-Electron Microscopy, Computational Biology, Bioinformatics, Computational Chemistry or a closely related field. Demonstrated experience in developing computational algorithms for solving problems. Demonstrated experience with computational methods development. Publications in macromolecular crystallography, cryo-electron microscopy or closely related fields. Good programming and mathematical skills, including familiarity with Python and other software development tools. Strong organizational skills including experience maintaining detailed and accurate records of experiment results and analyzed data. Excellent oral and written communication skills including experience organizing/presenting technical reports. Demonstrated interpersonal skills including experience conducting experiments independently and collaborating with a diverse interdisciplinary research team. Desired Qualifications: Experience with machine learning methods, programming with C++, or equivalent object-oriented programming languages. Experience with the practical aspects of crystallography and/or cryo-electron microscopy. Familiarity with macromolecular structure or computational chemistry. -- 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 [ MEEspinosa(a)lbl.gov ][ 1-510-333-6788 ] Phenix Consortium: Ashley Dawn [ AshleyDawn(a)lbl.gov ][ 1-510-486-5455 ] --

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Error in Windows installation: Phenix 1.21.2-54
by Jobichen Chacko 18 Jan '25

18 Jan '25

ImportError : __import__("gltbx_glu_ext"): DLL load failed while importing gltbx_glu_ext: A dynamic link library (DLL) initialization routine failed. sys.path: C:\ProgramData\phenix-1.21.2-5419\lib\site-packages\libsvm C:\ProgramData\phenix-1.21.2-5419\lib\site-packages\phenix\wxGUI2\command_line C:\ProgramData\phenix-1.21.2-5419\python39.zip C:\ProgramData\phenix-1.21.2-5419\DLLs C:\ProgramData\phenix-1.21.2-5419\lib C:\ProgramData\phenix-1.21.2-5419 C:\ProgramData\phenix-1.21.2-5419\lib\site-packages C:\ProgramData\phenix-1.21.2-5419\lib\site-packages\mmtbx\suitename Traceback (most recent call last): File "C:\ProgramData\phenix-1.21.2-5419\lib\site-packages\boost_adaptbx\boost\python.py", line 22, in import_ext try: mod = __import__(name) ImportError: DLL load failed while importing gltbx_glu_ext: A dynamic link library (DLL) initialization routine failed. During handling of the above exception, another exception occurred: Traceback (most recent call last): File "C:\ProgramData\phenix-1.21.2-5419\lib\site-packages\wxGUI2\MainWindow.py", line 745, in <lambda> menu.add_command("Run now", lambda evt: self.run()) File "C:\ProgramData\phenix-1.21.2-5419\lib\site-packages\wxGUI2\Programs\Refine\Main.py", line 426, in run self.start_process(config_file, output_dir, process_type) File "C:\ProgramData\phenix-1.21.2-5419\lib\site-packages\wxGUI2\Templates.py", line 701, in start_process run_notebook = self.create_run_notebook() File "C:\ProgramData\phenix-1.21.2-5419\lib\site-packages\wxGUI2\Programs\Refine\Main.py", line 532, in create_run_notebook from wxGUI2.Programs.Refine import Output File "C:\ProgramData\phenix-1.21.2-5419\lib\site-packages\wxGUI2\Programs\Refine\Output.py", line 5, in <module> from wxGUI2 import GLViewer, AdvancedWidgets, Buttons File "C:\ProgramData\phenix-1.21.2-5419\lib\site-packages\wxGUI2\GLViewer.py", line 10, in <module> from crys3d.wx_combined_viewer import viewer_phil File "C:\ProgramData\phenix-1.21.2-5419\lib\site-packages\crys3d\wx_combined_viewer.py", line 4, in <module> from crys3d.wx_selection_editor import selection_editor_mixin File "C:\ProgramData\phenix-1.21.2-5419\lib\site-packages\crys3d\wx_selection_editor.py", line 6, in <module> from crys3d.wx_model_viewer import model_scene, model_viewer_mixin File "C:\ProgramData\phenix-1.21.2-5419\lib\site-packages\crys3d\wx_model_viewer.py", line 10, in <module> from gltbx.wx_viewer import wxGLWindow File "C:\ProgramData\phenix-1.21.2-5419\lib\site-packages\gltbx\wx_viewer.py", line 8, in <module> from gltbx.glu import * File "C:\ProgramData\phenix-1.21.2-5419\lib\site-packages\gltbx\glu.py", line 3, in <module> ext = bp.import_ext("gltbx_glu_ext") File "C:\ProgramData\phenix-1.21.2-5419\lib\site-packages\boost_adaptbx\boost\python.py", line 31, in import_ext raise ImportError( Dear All, I am getting this error when trying to run Phenix-refine. Any idea how to fix this? Thank you. Jobi ImportError: __import__("gltbx_glu_ext"): DLL load failed while importing gltbx_glu_ext: A dynamic link library (DLL) initialization routine failed. sys.path: C:\ProgramData\phenix-1.21.2-5419\lib\site-packages\libsvm C:\ProgramData\phenix-1.21.2-5419\lib\site-packages\phenix\wxGUI2\command_line C:\ProgramData\phenix-1.21.2-5419\python39.zip C:\ProgramData\phenix-1.21.2-5419\DLLs C:\ProgramData\phenix-1.21.2-5419\lib C:\ProgramData\phenix-1.21.2-5419 C:\ProgramData\phenix-1.21.2-5419\lib\site-packages C:\ProgramData\phenix-1.21.2-5419\lib\site-packages\mmtbx\suitename

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Error opening REEL and ligand refinement in Coot
by Marian Oliva 17 Jan '25

17 Jan '25

Dear all, I posted this problem a couple of days ago through phenix help mail address but I got no answer (not sure if it was delivered properly). Maybe here I am luckier. I have recently upgrade my machine to Ubuntu MATE 1.26 and re-install all crystallography software I often use, including Phenix version dev-5493. I am working in a structure of a protein bound to a new ligand. I built the ligand with chemDraw, get the SMILE, get a universal SMILE string in cactus.nci.nih.gov <http://cactus.nci.nih.gov/>, and used eLbow for ligand restraints generation and optimization (using default parameters). First problem. When I try to open the ligand in REEL. Phenix crash with the following message in the terminal libGL error: MESA-LOADER: failed to open nouveau: /usr/lib/dri/nouveau_dri.so <http://nouveau_dri.so/>: cannot open shared object file: No such file or directory (search paths /usr/lib/x86_64-linux-gnu/dri:\$${ORIGIN}/dri:/usr/lib/dri, suffix _dri) libGL error: failed to load driver: nouveau libGL error: MESA-LOADER: failed to open nouveau: /usr/lib/dri/nouveau_dri.so <http://nouveau_dri.so/>: cannot open shared object file: No such file or directory (search paths /usr/lib/x86_64-linux-gnu/dri:\$${ORIGIN}/dri:/usr/lib/dri, suffix _dri) libGL error: failed to load driver: nouveau libGL error: MESA-LOADER: failed to open swrast: /usr/lib/dri/swrast_dri.so <http://swrast_dri.so/>: cannot open shared object file: No such file or directory (search paths /usr/lib/x86_64-linux-gnu/dri:\$${ORIGIN}/dri:/usr/lib/dri, suffix _dri) libGL error: failed to load driver: swrast The program 'main.py' received an X Window System error. This probably reflects a bug in the program. The error was 'BadValue'. (Details: serial 39668 error_code 2 request_code 152 minor_code 24) (Note to programmers: normally, X errors are reported asynchronously; that is, you will receive the error a while after causing it. To debug your program, run it with the --sync command line option to change this behavior. You can then get a meaningful backtrace from your debugger if you break on the gdk_x_error() function.) Second, when I open the structure in Coot (0.9.8.95) from Phenix and try to perform real space refine zone to the ligand, the attached window pops-up. Is this because I did something wrong during the installation? Is there a bug I am not aware of? Any help will be really appreciate. Many thanks in advance, Marian

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mmtbx.ringer with noise maps
by Schulz, Dr. Eike 15 Jan '25

15 Jan '25

Hi everyone, I am using mmtbx.ringer via phenix-1.21rc1-5127 to explore ED changes from END/RAPID maps. While it’s possible to provide volume scaled maps, it does seem possible to provide noise maps from END/RAPID is that correct or am I missing sth.? Related: setting gui=true enables to graphically browse through the results, it does not seem to be possible to automatically save all these plots. Is it possible to activate this? Best regards, Eike

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phenix.predict_and_build, proccess normal and no error, but not generate the PredictAndBuild_0_overall_best.pdb
by fnsoxt＠qq.com 09 Jan '25

09 Jan '25

How can i deal with it? This is the log file Starting phenix.predict_and_build on Wed Jan 1 20:55:50 2025 by xukui =============================================================================== Processing files: ------------------------------------------------------------------------------- No files found Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- full_map=/data2/xukui/data/jobs_pab/6b3o/6b3o.mrc seq_file=/data2/xukui/data/jobs_pab/6b3o/6b3o.fasta resolution=4.1 nproc=20 predicted_model=/data2/xukui/data/jobs_pab/6b3o/templ_af2/af2_group_0.pdb process_predicted_model.chunk_size=10000 predict_and_build.chunk_size=10000 process_predicted_model.break_into_chunks_if_length_is=10000 predict_and_build.break_into_chunks_if_length_is=10000 Warning: Ambiguous parameter definition: resolution = 4.1 Best matches: crystal_info.resolution prediction.resolution Assuming crystal_info.resolution was intended. Warning: Ambiguous parameter definition: nproc = 20 Best matches: prediction.nproc control.nproc Assuming control.nproc was intended. Processing files from PHIL: ------------------------------------------------------------------------------- Found model, /data2/xukui/data/jobs_pab/6b3o/templ_af2/af2_group_0.pdb Found sequence, /data2/xukui/data/jobs_pab/6b3o/6b3o.fasta Found real_map, /data2/xukui/data/jobs_pab/6b3o/6b3o.mrc Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { sequence_files = "/data2/xukui/data/jobs_pab/6b3o/6b3o.fasta" default_sequence = "/data2/xukui/data/jobs_pab/6b3o/6b3o.fasta" real_map_files = "/data2/xukui/data/jobs_pab/6b3o/6b3o.mrc" default_real_map = "/data2/xukui/data/jobs_pab/6b3o/6b3o.mrc" model { file = "/data2/xukui/data/jobs_pab/6b3o/templ_af2/af2_group_0.pdb" } default_model = "/data2/xukui/data/jobs_pab/6b3o/templ_af2/af2_group_0.pdb" } predict_and_build { break_into_chunks_if_length_is = 10000 chunk_size = 10000 } input_files { seq_file = /data2/xukui/data/jobs_pab/6b3o/6b3o.fasta map_model { full_map = /data2/xukui/data/jobs_pab/6b3o/6b3o.mrc } predicted_model = /data2/xukui/data/jobs_pab/6b3o/templ_af2/af2_group_0.pdb } crystal_info { resolution = 4.1 } process_predicted_model { break_into_chunks_if_length_is = 10000 chunk_size = 10000 } control { nproc = 20 } Starting job =============================================================================== ************************************************************ PHENIX predict_and_build Wed Jan 1 20:55:59 2025 ************************************************************ Working directory: /data2/xukui/data/jobs_pab/6b3o PHENIX VERSION: 1.21.1-5286 Base directory is /data2/xukui/data/jobs_pab/6b3o Creating jobname of 'PredictAndBuild_0' Working directory /data2/xukui/data/jobs_pab/6b3o/PredictAndBuild_0_CarryOn will be created in base directory Output prefix for files will be: /data2/xukui/data/jobs_pab/6b3o/PredictAndBuild_0_CarryOn/PredictAndBuild_0_rebuilt Running in Standard mode... Turning off all building steps except refinement Running with a cryo-EM map Mean B-iso in af2_group_0.pdb: 80.9577007535 A**2 Added predicted model /data2/xukui/data/jobs_pab/6b3o/templ_af2/af2_group_0.pdb_A with plddt=80.96 Mean value in B-factor field for /data2/xukui/data/jobs_pab/6b3o/templ_af2/af2_group_0.pdb (converted from plddt to plddt): 80.96 Set random_seed_iterations to 5 No templates read from templates_as_string... Total of 0 templates to be used Setting density_modify_with_model = False (default for cryo-EM) Set rmsd_for_similar_placement to 4.10 A Working directory will be based on jobname: PredictAndBuild_0 Created new temp dir: PredictAndBuild_0 ... temp-dir will be deleted at end ================================================================================ Running predict_and_build ================================================================================ Starting data: Map file: Map manager (from /data2/xukui/data/jobs_pab/6b3o/6b3o.mrc) Unit cell: (435.2, 435.2, 435.2, 90, 90, 90) Space group: P 1 (No. 1), Unit-cell grid: (320, 320, 320), (present: (320, 320, 320)), origin shift (0, 0, 0) Working coordinate shift (-0.0, -0.0, -0.0) NCS object with 0 groups: List of sequences: MKLCILLAVVAFVGLSLGRSLASVSTGYRLTTFEPYTPMLVNDSVQSVDGLYEMQIPTNFTIGHHEEFIQTRSPKVTIDCAAFVCGDNTACRQQLVEYGSFCVNVNAILNEVNNLLDNMQLQVASALMQGVTISSRLPDGISGPIDDINFSPLLGCIGSTCAEDGNGPSAIRGRSAIEDLLFDKVKLSDVGFVEAYNNCTGGQEVRDLLCVQSFNGIKVLPPVLSESQISGYTTGATAAAMFPPWSAAAGVPFSLSVQYRINGLGVTMNVLSENQKMIASAFNNALGAIQDGFDATNSALGKIQSVVNANAEALNNLLNQLSNRFGAISASLQEILTRLEAVEAKAQIDRLINGRLTALNAYISKQLSDSTLIKVSAAQAIEKVNECVKSQTTRINFCGNGNHILSLVQNAPYGLYFIHFSYVPISFTTANVSPGLCISGDRGLAPKAGYFVQDDGEWKFTGSSYYYPEPITDKNSVIMSSCAVNYTKAPEVFLNTSIPNPPDFKEELDKWFKNQTSIAPDLSLDFEKLNVTLLDLTYEMNRIQDAIKKLNESYINLIKRMKQIEDKIEEIESKQKKIENEIARIKKIKLVPRGSLEWSHPQFEK MKLCILLAVVAFVGLSLGRSLASVSTGYRLTTFEPYTPMLVNDSVQSVDGLYEMQIPTNFTIGHHEEFIQTRSPKVTIDCAAFVCGDNTACRQQLVEYGSFCVNVNAILNEVNNLLDNMQLQVASALMQGVTISSRLPDGISGPIDDINFSPLLGCIGSTCAEDGNGPSAIRGRSAIEDLLFDKVKLSDVGFVEAYNNCTGGQEVRDLLCVQSFNGIKVLPPVLSESQISGYTTGATAAAMFPPWSAAAGVPFSLSVQYRINGLGVTMNVLSENQKMIASAFNNALGAIQDGFDATNSALGKIQSVVNANAEALNNLLNQLSNRFGAISASLQEILTRLEAVEAKAQIDRLINGRLTALNAYISKQLSDSTLIKVSAAQAIEKVNECVKSQTTRINFCGNGNHILSLVQNAPYGLYFIHFSYVPISFTTANVSPGLCISGDRGLAPKAGYFVQDDGEWKFTGSSYYYPEPITDKNSVIMSSCAVNYTKAPEVFLNTSIPNPPDFKEELDKWFKNQTSIAPDLSLDFEKLNVTLLDLTYEMNRIQDAIKKLNESYINLIKRMKQIEDKIEEIESKQKKIENEIARIKKIKLVPRGSLEWSHPQFEK MKLCILLAVVAFVGLSLGRSLASVSTGYRLTTFEPYTPMLVNDSVQSVDGLYEMQIPTNFTIGHHEEFIQTRSPKVTIDCAAFVCGDNTACRQQLVEYGSFCVNVNAILNEVNNLLDNMQLQVASALMQGVTISSRLPDGISGPIDDINFSPLLGCIGSTCAEDGNGPSAIRGRSAIEDLLFDKVKLSDVGFVEAYNNCTGGQEVRDLLCVQSFNGIKVLPPVLSESQISGYTTGATAAAMFPPWSAAAGVPFSLSVQYRINGLGVTMNVLSENQKMIASAFNNALGAIQDGFDATNSALGKIQSVVNANAEALNNLLNQLSNRFGAISASLQEILTRLEAVEAKAQIDRLINGRLTALNAYISKQLSDSTLIKVSAAQAIEKVNECVKSQTTRINFCGNGNHILSLVQNAPYGLYFIHFSYVPISFTTANVSPGLCISGDRGLAPKAGYFVQDDGEWKFTGSSYYYPEPITDKNSVIMSSCAVNYTKAPEVFLNTSIPNPPDFKEELDKWFKNQTSIAPDLSLDFEKLNVTLLDLTYEMNRIQDAIKKLNESYINLIKRMKQIEDKIEEIESKQKKIENEIARIKKIKLVPRGSLEWSHPQFEK List of models: af2_group_0.pdb Chain A extracted List of chain IDs and sequences to use A (6b3o_A): MKLCILLAVVAFVGLSLGRSLASVSTGYRLTTFEPYTPMLVNDSVQSVDGLYEMQIPTNFTIGHHEEFIQTRSPKVTIDCAAFVCGDNTACRQQLVEYGSFCVNVNAILNEVNNLLDNMQLQVASALMQGVTISSRLPDGISGPIDDINFSPLLGCIGSTCAEDGNGPSAIRGRSAIEDLLFDKVKLSDVGFVEAYNNCTGGQEVRDLLCVQSFNGIKVLPPVLSESQISGYTTGATAAAMFPPWSAAAGVPFSLSVQYRINGLGVTMNVLSENQKMIASAFNNALGAIQDGFDATNSALGKIQSVVNANAEALNNLLNQLSNRFGAISASLQEILTRLEAVEAKAQIDRLINGRLTALNAYISKQLSDSTLIKVSAAQAIEKVNECVKSQTTRINFCGNGNHILSLVQNAPYGLYFIHFSYVPISFTTANVSPGLCISGDRGLAPKAGYFVQDDGEWKFTGSSYYYPEPITDKNSVIMSSCAVNYTKAPEVFLNTSIPNPPDFKEELDKWFKNQTSIAPDLSLDFEKLNVTLLDLTYEMNRIQDAIKKLNESYINLIKRMKQIEDKIEEIESKQKKIENEIARIKKIKLVPRGSLEWSHPQFEK B (6b3o_A): MKLCILLAVVAFVGLSLGRSLASVSTGYRLTTFEPYTPMLVNDSVQSVDGLYEMQIPTNFTIGHHEEFIQTRSPKVTIDCAAFVCGDNTACRQQLVEYGSFCVNVNAILNEVNNLLDNMQLQVASALMQGVTISSRLPDGISGPIDDINFSPLLGCIGSTCAEDGNGPSAIRGRSAIEDLLFDKVKLSDVGFVEAYNNCTGGQEVRDLLCVQSFNGIKVLPPVLSESQISGYTTGATAAAMFPPWSAAAGVPFSLSVQYRINGLGVTMNVLSENQKMIASAFNNALGAIQDGFDATNSALGKIQSVVNANAEALNNLLNQLSNRFGAISASLQEILTRLEAVEAKAQIDRLINGRLTALNAYISKQLSDSTLIKVSAAQAIEKVNECVKSQTTRINFCGNGNHILSLVQNAPYGLYFIHFSYVPISFTTANVSPGLCISGDRGLAPKAGYFVQDDGEWKFTGSSYYYPEPITDKNSVIMSSCAVNYTKAPEVFLNTSIPNPPDFKEELDKWFKNQTSIAPDLSLDFEKLNVTLLDLTYEMNRIQDAIKKLNESYINLIKRMKQIEDKIEEIESKQKKIENEIARIKKIKLVPRGSLEWSHPQFEK C (6b3o_A): MKLCILLAVVAFVGLSLGRSLASVSTGYRLTTFEPYTPMLVNDSVQSVDGLYEMQIPTNFTIGHHEEFIQTRSPKVTIDCAAFVCGDNTACRQQLVEYGSFCVNVNAILNEVNNLLDNMQLQVASALMQGVTISSRLPDGISGPIDDINFSPLLGCIGSTCAEDGNGPSAIRGRSAIEDLLFDKVKLSDVGFVEAYNNCTGGQEVRDLLCVQSFNGIKVLPPVLSESQISGYTTGATAAAMFPPWSAAAGVPFSLSVQYRINGLGVTMNVLSENQKMIASAFNNALGAIQDGFDATNSALGKIQSVVNANAEALNNLLNQLSNRFGAISASLQEILTRLEAVEAKAQIDRLINGRLTALNAYISKQLSDSTLIKVSAAQAIEKVNECVKSQTTRINFCGNGNHILSLVQNAPYGLYFIHFSYVPISFTTANVSPGLCISGDRGLAPKAGYFVQDDGEWKFTGSSYYYPEPITDKNSVIMSSCAVNYTKAPEVFLNTSIPNPPDFKEELDKWFKNQTSIAPDLSLDFEKLNVTLLDLTYEMNRIQDAIKKLNESYINLIKRMKQIEDKIEEIESKQKKIENEIARIKKIKLVPRGSLEWSHPQFEK ================================================================================ Running cycle 1 of predict_and_build ================================================================================ Not using any supplied msas No supplied templates will be used in prediction this cycle ================================================================================ Predicting models for 0 chains with alphafold Updating chain names in model list... Chain A: MKLCILLAVVAFVGLSLGRSLASVSTGYRLTTFEPYTPMLVNDSVQSVDGLYEMQIPTNFTIGHHEEFIQTRSPKVTIDCAAFVCGDNTACRQQLVEYGSFCVNVNAILNEVNNLLDNMQLQVASALMQGVTISSRLPDGISGPIDDINFSPLLGCIGSTCAEDGNGPSAIRGRSAIEDLLFDKVKLSDVGFVEAYNNCTGGQEVRDLLCVQSFNGIKVLPPVLSESQISGYTTGATAAAMFPPWSAAAGVPFSLSVQYRINGLGVTMNVLSENQKMIASAFNNALGAIQDGFDATNSALGKIQSVVNANAEALNNLLNQLSNRFGAISASLQEILTRLEAVEAKAQIDRLINGRLTALNAYISKQLSDSTLIKVSAAQAIEKVNECVKSQTTRINFCGNGNHILSLVQNAPYGLYFIHFSYVPISFTTANVSPGLCISGDRGLAPKAGYFVQDDGEWKFTGSSYYYPEPITDKNSVIMSSCAVNYTKAPEVFLNTSIPNPPDFKEELDKWFKNQTSIAPDLSLDFEKLNVTLLDLTYEMNRIQDAIKKLNESYINLIKRMKQIEDKIEEIESKQKKIENEIARIKKIKLVPRGSLEWSHPQFEK Total of 1 working models Total MSAs obtained: 0 Updating chain IDs Previous ID: 'A' New ID: 'A' MODEL: af2_group_0.pdb Getting processed (trimmed, B-values updated) models B-value field interpreted as pLDDT (0 - 100) Maximum rmsd of 1.50 A used Maximum B-value to be included: 59.22 A**2 Removing short segments: (chain A and resseq 537:539) Total of 492 of 605 residues kept after B-factor filtering Selection string for B-factor filtering: (chain A and resseq 15:20) or (chain A and resseq 25:136) or (chain A and resseq 145:157) or (chain A and resseq 174:200) or (chain A and resseq 207:494) or (chain A and resseq 541:586) Selecting domains as compact chains Clusters: 15 Threshold: 3.90 Clusters: 5 Threshold: 4.40 Clusters: 6 Threshold: 4.82 Clusters: 5 Threshold: 4.34 Clusters: 3 Threshold: 3.27 Clusters: 2 Threshold: 2.14 Clusters: 3 Threshold: 3.98 Clusters: 2 Threshold: 1.81 Clusters: 3 Threshold: 3.74 Clusters: 2 Threshold: 1.80 Best resolution for domains is 35.0 A giving 3 regions Selection list based on domains: (resseq 15:20) or (resseq 25:136) or (resseq 145:157) or (resseq 174:200) or (resseq 207:494) or (resseq 541:586) (492 residues) Total of 1 regions identified Obtained processed model from af2_group_0.pdb with 492 residues (of 605) =============================================================================== Finished with prediction (Job PredictAndBuild_0 cycle 1 at 2025-01-01 20:56:19) =============================================================================== =============================================================================== Getting scaffold model... (Job PredictAndBuild_0 cycle 1 at 2025-01-01 20:56:19) =============================================================================== Checking whether scaffold model is complete... ================================================================================ Getting new scaffold model in /data2/xukui/data/jobs_pab/6b3o/PredictAndBuild_0_CarryOn/PredictAndBuild_0_scaffold_cycle_1.pdb ================================================================================ ================================================================================ Docking 1 models (to represent 3 sequences) in map to create a scaffold ================================================================================ Model to dock: af2_group_0.pdb: MKLCILLAVVAFVGLSLGRSLASVSTGYRLTTFEPYTPMLVNDSVQSVDGLYEMQIPTNFTIGHHEEFIQTRSPKVTIDCAAFVCGDNTACRQQLVEYGSFCVNVNAILNEVNNLLDNMQLQVASALMQGVTISSRLPDGISGPIDDINFSPLLGCIGSTCAEDGNGPSAIRGRSAIEDLLFDKVKLSDVGFVEAYNNCTGGQEVRDLLCVQSFNGIKVLPPVLSESQISGYTTGATAAAMFPPWSAAAGVPFSLSVQYRINGLGVTMNVLSENQKMIASAFNNALGAIQDGFDATNSALGKIQSVVNANAEALNNLLNQLSNRFGAISASLQEILTRLEAVEAKAQIDRLINGRLTALNAYISKQLSDSTLIKVSAAQAIEKVNECVKSQTTRINFCGNGNHILSLVQNAPYGLYFIHFSYVPISFTTANVSPGLCISGDRGLAPKAGYFVQDDGEWKFTGSSYYYPEPITDKNSVIMSSCAVNYTKAPEVFLNTSIPNPPDFKEELDKWFKNQTSIAPDLSLDFEKLNVTLLDLTYEMNRIQDAIKKLNESYINLIKRMKQIEDKIEEIESKQKKIENEIARIKKIKLVPRGSLEWSHPQFEK Calculating how many copies of each sequence Model: A MKLCILLAVVAFVGLSLGRSLASVSTGYRLTTFEPYTPMLVNDSVQSVDGLYEMQIPTNFTIGHHEEFIQTRSPKVTIDCAAFVCGDNTACRQQLVEYGSFCVNVNAILNEVNNLLDNMQLQVASALMQGVTISSRLPDGISGPIDDINFSPLLGCIGSTCAEDGNGPSAIRGRSAIEDLLFDKVKLSDVGFVEAYNNCTGGQEVRDLLCVQSFNGIKVLPPVLSESQISGYTTGATAAAMFPPWSAAAGVPFSLSVQYRINGLGVTMNVLSENQKMIASAFNNALGAIQDGFDATNSALGKIQSVVNANAEALNNLLNQLSNRFGAISASLQEILTRLEAVEAKAQIDRLINGRLTALNAYISKQLSDSTLIKVSAAQAIEKVNECVKSQTTRINFCGNGNHILSLVQNAPYGLYFIHFSYVPISFTTANVSPGLCISGDRGLAPKAGYFVQDDGEWKFTGSSYYYPEPITDKNSVIMSSCAVNYTKAPEVFLNTSIPNPPDFKEELDKWFKNQTSIAPDLSLDFEKLNVTLLDLTYEMNRIQDAIKKLNESYINLIKRMKQIEDKIEEIESKQKKIENEIARIKKIKLVPRGSLEWSHPQFEK Model copies: 1 Sequence copies: 3 Remainder copies: {'MKLCILLAVVAFVGLSLGRSLASVSTGYRLTTFEPYTPMLVNDSVQSVDGLYEMQIPTNFTIGHHEEFIQTRSPKVTIDCAAFVCGDNTACRQQLVEYGSFCVNVNAILNEVNNLLDNMQLQVASALMQGVTISSRLPDGISGPIDDINFSPLLGCIGSTCAEDGNGPSAIRGRSAIEDLLFDKVKLSDVGFVEAYNNCTGGQEVRDLLCVQSFNGIKVLPPVLSESQISGYTTGATAAAMFPPWSAAAGVPFSLSVQYRINGLGVTMNVLSENQKMIASAFNNALGAIQDGFDATNSALGKIQSVVNANAEALNNLLNQLSNRFGAISASLQEILTRLEAVEAKAQIDRLINGRLTALNAYISKQLSDSTLIKVSAAQAIEKVNECVKSQTTRINFCGNGNHILSLVQNAPYGLYFIHFSYVPISFTTANVSPGLCISGDRGLAPKAGYFVQDDGEWKFTGSSYYYPEPITDKNSVIMSSCAVNYTKAPEVFLNTSIPNPPDFKEELDKWFKNQTSIAPDLSLDFEKLNVTLLDLTYEMNRIQDAIKKLNESYINLIKRMKQIEDKIEEIESKQKKIENEIARIKKIKLVPRGSLEWSHPQFEK': 0} remainder: 0 Copies to use: 3 Setting up model for dock_and_rebuild Added model af2_group_0.pdb (A) for dock_and_rebuild Running dock_and_rebuild to dock models Total of 1 predicted models MODEL: MKLCILLAVVAFVGLSLGRSLASVSTGYRLTTFEPYTPMLVNDSVQSVDGLYEMQIPTNFTIGHHEEFIQTRSPKVTIDCAAFVCGDNTACRQQLVEYGSFCVNVNAILNEVNNLLDNMQLQVASALMQGVTISSRLPDGISGPIDDINFSPLLGCIGSTCAEDGNGPSAIRGRSAIEDLLFDKVKLSDVGFVEAYNNCTGGQEVRDLLCVQSFNGIKVLPPVLSESQISGYTTGATAAAMFPPWSAAAGVPFSLSVQYRINGLGVTMNVLSENQKMIASAFNNALGAIQDGFDATNSALGKIQSVVNANAEALNNLLNQLSNRFGAISASLQEILTRLEAVEAKAQIDRLINGRLTALNAYISKQLSDSTLIKVSAAQAIEKVNECVKSQTTRINFCGNGNHILSLVQNAPYGLYFIHFSYVPISFTTANVSPGLCISGDRGLAPKAGYFVQDDGEWKFTGSSYYYPEPITDKNSVIMSSCAVNYTKAPEVFLNTSIPNPPDFKEELDKWFKNQTSIAPDLSLDFEKLNVTLLDLTYEMNRIQDAIKKLNESYINLIKRMKQIEDKIEEIESKQKKIENEIARIKKIKLVPRGSLEWSHPQFEK ================================================================================ Running dock_and_rebuild on total of 3 chains Chain 1 (chain A from af2_group_0.pdb) Chain 2 (chain A from af2_group_0.pdb) Chain 3 (chain A from af2_group_0.pdb) ================================================================================ ================================================================================ Running on chain 1 (chain A from af2_group_0.pdb) ================================================================================ Working directory for this chain: PredictAndBuild_0/local_dock_and_rebuild_1_0 No docked model for chain A ... Running search... Running standard docking... =============================================================================== Processing input model =============================================================================== B-value field interpreted as pLDDT (0 - 100) Maximum rmsd of 1.50 A used Maximum B-value to be included: 59.22 A**2 Removing short segments: (chain A and resseq 537:539) Total of 492 of 605 residues kept after B-factor filtering Selection string for B-factor filtering: (chain A and resseq 15:20) or (chain A and resseq 25:136) or (chain A and resseq 145:157) or (chain A and resseq 174:200) or (chain A and resseq 207:494) or (chain A and resseq 541:586) Selecting domains as compact chains Clusters: 15 Threshold: 3.90 Clusters: 5 Threshold: 4.40 Clusters: 6 Threshold: 4.82 Clusters: 5 Threshold: 4.34 Clusters: 3 Threshold: 3.27 Clusters: 2 Threshold: 2.14 Clusters: 3 Threshold: 3.98 Clusters: 2 Threshold: 1.81 Clusters: 3 Threshold: 3.74 Clusters: 2 Threshold: 1.80 Best resolution for domains is 35.0 A giving 3 regions Selection list based on domains: (resseq 15:20) or (resseq 25:136) or (resseq 145:157) or (resseq 174:200) or (resseq 207:494) or (resseq 541:586) (492 residues) Total of 1 regions identified Obtained processed model with 492 residues (of 605) Wrote processed model to /data2/xukui/data/jobs_pab/6b3o/PredictAndBuild_0/local_dock_and_rebuild_1_0/working_model_processed.pdb =============================================================================== Extracting unique part of map =============================================================================== Setting map-model-manager and model shift to zero during run Split model into chains: A1 Chain number: 1 id: A1 Residues: 492 ============================================================================== Searching with each chain as a seed ============================================================================== ============================================================================== Running dock-in map on domain A1 with 492 residues ============================================================================== Running dock-in-map at overall resolution of 4.1 A Density radius set to: 24.6 A Placing model in map Map has been not been offset New cell after running map_box: (435.20, 424.32, 435.20, 90.00, 90.00, 90.00) Target boxes set to 20 Choosing local part of search model to use in search... Shifting search model coordinates (0.3, 1.9, -1.9) to origin and creating search map coefficients Docking with MR... Using masked map data MODEL: full_shifted_sm_1.pdb mass: 54120 (copies: 1) Estimated solvent fraction: 0.95 Total atoms in all copies: 3781 (volume = 66567.6 A**3) Solvent fraction (as used) is about 0.94 Total good sites: 11268 Max clusters: 1 Wrote mtz data to PredictAndBuild_0/local_dock_and_rebuild_1_0/run_mr/mtz_data.mtz Wrote model A1_full_shifted_sm_1.pdb to PredictAndBuild_0/local_dock_and_rebuild_1_0/run_mr/A1_full_shifted_sm_1.pdb Wrote model A_from_cluster_0.pdb to PredictAndBuild_0/local_dock_and_rebuild_1_0/run_mr/A_from_cluster_0.pdb

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Re: phenix.predict_and_build, proccess normal and no error, but not generate the PredictAndBuild_0_overall_best.pdb
by Tom Terwilliger 09 Jan '25

09 Jan '25

On Thu, Jan 9, 2025 at 11:13 AM Oleg Sobolev <osobolev(a)lbl.gov> wrote: > Hi Tom, > > I fished out the following from my Spam folder, but it is on PhenixBB. Can > you please take a look? > > Best regards, > Oleg Sobolev. > > ---------- Forwarded message --------- > From: <fnsoxt(a)qq.com> > Date: Sun, Jan 5, 2025 at 8:03 PM > Subject: [phenixbb] phenix.predict_and_build, proccess normal and no > error, but not generate the PredictAndBuild_0_overall_best.pdb > To: <phenixbb(a)phenix-online.org> > > > How can i deal with it? This is the log file > > Starting phenix.predict_and_build > on Wed Jan 1 20:55:50 2025 by xukui > > =============================================================================== > > Processing files: > > ------------------------------------------------------------------------------- > > No files found > > Processing PHIL parameters: > > ------------------------------------------------------------------------------- > > Adding command-line PHIL: > ------------------------- > full_map=/data2/xukui/data/jobs_pab/6b3o/6b3o.mrc > seq_file=/data2/xukui/data/jobs_pab/6b3o/6b3o.fasta > resolution=4.1 > nproc=20 > > predicted_model=/data2/xukui/data/jobs_pab/6b3o/templ_af2/af2_group_0.pdb > process_predicted_model.chunk_size=10000 > predict_and_build.chunk_size=10000 > process_predicted_model.break_into_chunks_if_length_is=10000 > predict_and_build.break_into_chunks_if_length_is=10000 > > Warning: Ambiguous parameter definition: resolution = 4.1 > Best matches: > crystal_info.resolution > prediction.resolution > Assuming crystal_info.resolution was intended. > Warning: Ambiguous parameter definition: nproc = 20 > Best matches: > prediction.nproc > control.nproc > Assuming control.nproc was intended. > Processing files from PHIL: > > ------------------------------------------------------------------------------- > > Found model, /data2/xukui/data/jobs_pab/6b3o/templ_af2/af2_group_0.pdb > Found sequence, /data2/xukui/data/jobs_pab/6b3o/6b3o.fasta > Found real_map, /data2/xukui/data/jobs_pab/6b3o/6b3o.mrc > > Final processed PHIL parameters: > > ------------------------------------------------------------------------------- > data_manager { > sequence_files = "/data2/xukui/data/jobs_pab/6b3o/6b3o.fasta" > default_sequence = "/data2/xukui/data/jobs_pab/6b3o/6b3o.fasta" > real_map_files = "/data2/xukui/data/jobs_pab/6b3o/6b3o.mrc" > default_real_map = "/data2/xukui/data/jobs_pab/6b3o/6b3o.mrc" > model { > file = "/data2/xukui/data/jobs_pab/6b3o/templ_af2/af2_group_0.pdb" > } > default_model = > "/data2/xukui/data/jobs_pab/6b3o/templ_af2/af2_group_0.pdb" > } > predict_and_build { > break_into_chunks_if_length_is = 10000 > chunk_size = 10000 > } > input_files { > seq_file = /data2/xukui/data/jobs_pab/6b3o/6b3o.fasta > map_model { > full_map = /data2/xukui/data/jobs_pab/6b3o/6b3o.mrc > } > predicted_model = > /data2/xukui/data/jobs_pab/6b3o/templ_af2/af2_group_0.pdb > } > crystal_info { > resolution = 4.1 > } > process_predicted_model { > break_into_chunks_if_length_is = 10000 > chunk_size = 10000 > } > control { > nproc = 20 > } > > > Starting job > > =============================================================================== > > ************************************************************ > PHENIX predict_and_build Wed Jan 1 20:55:59 2025 > ************************************************************ > > Working directory: /data2/xukui/data/jobs_pab/6b3o > > PHENIX VERSION: 1.21.1-5286 > > Base directory is /data2/xukui/data/jobs_pab/6b3o > Creating jobname of 'PredictAndBuild_0' > Working directory > /data2/xukui/data/jobs_pab/6b3o/PredictAndBuild_0_CarryOn will be created > in base directory > Output prefix for files will be: > /data2/xukui/data/jobs_pab/6b3o/PredictAndBuild_0_CarryOn/PredictAndBuild_0_rebuilt > Running in Standard mode... > Turning off all building steps except refinement > > Running with a cryo-EM map > Mean B-iso in af2_group_0.pdb: 80.9577007535 A**2 > Added predicted model > /data2/xukui/data/jobs_pab/6b3o/templ_af2/af2_group_0.pdb_A with > plddt=80.96 > Mean value in B-factor field for > /data2/xukui/data/jobs_pab/6b3o/templ_af2/af2_group_0.pdb (converted from > plddt to plddt): 80.96 > Set random_seed_iterations to 5 > No templates read from templates_as_string... > Total of 0 templates to be used > Setting density_modify_with_model = False (default for cryo-EM) > > Set rmsd_for_similar_placement to 4.10 A > Working directory will be based on jobname: PredictAndBuild_0 > Created new temp dir: PredictAndBuild_0 ... > temp-dir will be deleted at end > > > ================================================================================ > Running predict_and_build > > ================================================================================ > > Starting data: > Map file: Map manager (from /data2/xukui/data/jobs_pab/6b3o/6b3o.mrc) > Unit cell: (435.2, 435.2, 435.2, 90, 90, 90) Space group: P 1 (No. 1), > Unit-cell grid: (320, 320, 320), (present: (320, 320, 320)), origin shift > (0, 0, 0) > Working coordinate shift (-0.0, -0.0, -0.0) > NCS object with 0 groups: > > List of sequences: > > MKLCILLAVVAFVGLSLGRSLASVSTGYRLTTFEPYTPMLVNDSVQSVDGLYEMQIPTNFTIGHHEEFIQTRSPKVTIDCAAFVCGDNTACRQQLVEYGSFCVNVNAILNEVNNLLDNMQLQVASALMQGVTISSRLPDGISGPIDDINFSPLLGCIGSTCAEDGNGPSAIRGRSAIEDLLFDKVKLSDVGFVEAYNNCTGGQEVRDLLCVQSFNGIKVLPPVLSESQISGYTTGATAAAMFPPWSAAAGVPFSLSVQYRINGLGVTMNVLSENQKMIASAFNNALGAIQDGFDATNSALGKIQSVVNANAEALNNLLNQLSNRFGAISASLQEILTRLEAVEAKAQIDRLINGRLTALNAYISKQLSDSTLIKVSAAQAIEKVNECVKSQTTRINFCGNGNHILSLVQNAPYGLYFIHFSYVPISFTTANVSPGLCISGDRGLAPKAGYFVQDDGEWKFTGSSYYYPEPITDKNSVIMSSCAVNYTKAPEVFLNTSIPNPPDFKEELDKWFKNQTSIAPDLSLDFEKLNVTLLDLTYEMNRIQDAIKKLNESYINLIKRMKQIEDKIEEIESKQKKIENEIARIKKIKLVPRGSLEWSHPQFEK > > MKLCILLAVVAFVGLSLGRSLASVSTGYRLTTFEPYTPMLVNDSVQSVDGLYEMQIPTNFTIGHHEEFIQTRSPKVTIDCAAFVCGDNTACRQQLVEYGSFCVNVNAILNEVNNLLDNMQLQVASALMQGVTISSRLPDGISGPIDDINFSPLLGCIGSTCAEDGNGPSAIRGRSAIEDLLFDKVKLSDVGFVEAYNNCTGGQEVRDLLCVQSFNGIKVLPPVLSESQISGYTTGATAAAMFPPWSAAAGVPFSLSVQYRINGLGVTMNVLSENQKMIASAFNNALGAIQDGFDATNSALGKIQSVVNANAEALNNLLNQLSNRFGAISASLQEILTRLEAVEAKAQIDRLINGRLTALNAYISKQLSDSTLIKVSAAQAIEKVNECVKSQTTRINFCGNGNHILSLVQNAPYGLYFIHFSYVPISFTTANVSPGLCISGDRGLAPKAGYFVQDDGEWKFTGSSYYYPEPITDKNSVIMSSCAVNYTKAPEVFLNTSIPNPPDFKEELDKWFKNQTSIAPDLSLDFEKLNVTLLDLTYEMNRIQDAIKKLNESYINLIKRMKQIEDKIEEIESKQKKIENEIARIKKIKLVPRGSLEWSHPQFEK > > MKLCILLAVVAFVGLSLGRSLASVSTGYRLTTFEPYTPMLVNDSVQSVDGLYEMQIPTNFTIGHHEEFIQTRSPKVTIDCAAFVCGDNTACRQQLVEYGSFCVNVNAILNEVNNLLDNMQLQVASALMQGVTISSRLPDGISGPIDDINFSPLLGCIGSTCAEDGNGPSAIRGRSAIEDLLFDKVKLSDVGFVEAYNNCTGGQEVRDLLCVQSFNGIKVLPPVLSESQISGYTTGATAAAMFPPWSAAAGVPFSLSVQYRINGLGVTMNVLSENQKMIASAFNNALGAIQDGFDATNSALGKIQSVVNANAEALNNLLNQLSNRFGAISASLQEILTRLEAVEAKAQIDRLINGRLTALNAYISKQLSDSTLIKVSAAQAIEKVNECVKSQTTRINFCGNGNHILSLVQNAPYGLYFIHFSYVPISFTTANVSPGLCISGDRGLAPKAGYFVQDDGEWKFTGSSYYYPEPITDKNSVIMSSCAVNYTKAPEVFLNTSIPNPPDFKEELDKWFKNQTSIAPDLSLDFEKLNVTLLDLTYEMNRIQDAIKKLNESYINLIKRMKQIEDKIEEIESKQKKIENEIARIKKIKLVPRGSLEWSHPQFEK > > List of models: > af2_group_0.pdb Chain A extracted > > List of chain IDs and sequences to use > A (6b3o_A): > MKLCILLAVVAFVGLSLGRSLASVSTGYRLTTFEPYTPMLVNDSVQSVDGLYEMQIPTNFTIGHHEEFIQTRSPKVTIDCAAFVCGDNTACRQQLVEYGSFCVNVNAILNEVNNLLDNMQLQVASALMQGVTISSRLPDGISGPIDDINFSPLLGCIGSTCAEDGNGPSAIRGRSAIEDLLFDKVKLSDVGFVEAYNNCTGGQEVRDLLCVQSFNGIKVLPPVLSESQISGYTTGATAAAMFPPWSAAAGVPFSLSVQYRINGLGVTMNVLSENQKMIASAFNNALGAIQDGFDATNSALGKIQSVVNANAEALNNLLNQLSNRFGAISASLQEILTRLEAVEAKAQIDRLINGRLTALNAYISKQLSDSTLIKVSAAQAIEKVNECVKSQTTRINFCGNGNHILSLVQNAPYGLYFIHFSYVPISFTTANVSPGLCISGDRGLAPKAGYFVQDDGEWKFTGSSYYYPEPITDKNSVIMSSCAVNYTKAPEVFLNTSIPNPPDFKEELDKWFKNQTSIAPDLSLDFEKLNVTLLDLTYEMNRIQDAIKKLNESYINLIKRMKQIEDKIEEIESKQKKIENEIARIKKIKLVPRGSLEWSHPQFEK > B (6b3o_A): > MKLCILLAVVAFVGLSLGRSLASVSTGYRLTTFEPYTPMLVNDSVQSVDGLYEMQIPTNFTIGHHEEFIQTRSPKVTIDCAAFVCGDNTACRQQLVEYGSFCVNVNAILNEVNNLLDNMQLQVASALMQGVTISSRLPDGISGPIDDINFSPLLGCIGSTCAEDGNGPSAIRGRSAIEDLLFDKVKLSDVGFVEAYNNCTGGQEVRDLLCVQSFNGIKVLPPVLSESQISGYTTGATAAAMFPPWSAAAGVPFSLSVQYRINGLGVTMNVLSENQKMIASAFNNALGAIQDGFDATNSALGKIQSVVNANAEALNNLLNQLSNRFGAISASLQEILTRLEAVEAKAQIDRLINGRLTALNAYISKQLSDSTLIKVSAAQAIEKVNECVKSQTTRINFCGNGNHILSLVQNAPYGLYFIHFSYVPISFTTANVSPGLCISGDRGLAPKAGYFVQDDGEWKFTGSSYYYPEPITDKNSVIMSSCAVNYTKAPEVFLNTSIPNPPDFKEELDKWFKNQTSIAPDLSLDFEKLNVTLLDLTYEMNRIQDAIKKLNESYINLIKRMKQIEDKIEEIESKQKKIENEIARIKKIKLVPRGSLEWSHPQFEK > C (6b3o_A): > MKLCILLAVVAFVGLSLGRSLASVSTGYRLTTFEPYTPMLVNDSVQSVDGLYEMQIPTNFTIGHHEEFIQTRSPKVTIDCAAFVCGDNTACRQQLVEYGSFCVNVNAILNEVNNLLDNMQLQVASALMQGVTISSRLPDGISGPIDDINFSPLLGCIGSTCAEDGNGPSAIRGRSAIEDLLFDKVKLSDVGFVEAYNNCTGGQEVRDLLCVQSFNGIKVLPPVLSESQISGYTTGATAAAMFPPWSAAAGVPFSLSVQYRINGLGVTMNVLSENQKMIASAFNNALGAIQDGFDATNSALGKIQSVVNANAEALNNLLNQLSNRFGAISASLQEILTRLEAVEAKAQIDRLINGRLTALNAYISKQLSDSTLIKVSAAQAIEKVNECVKSQTTRINFCGNGNHILSLVQNAPYGLYFIHFSYVPISFTTANVSPGLCISGDRGLAPKAGYFVQDDGEWKFTGSSYYYPEPITDKNSVIMSSCAVNYTKAPEVFLNTSIPNPPDFKEELDKWFKNQTSIAPDLSLDFEKLNVTLLDLTYEMNRIQDAIKKLNESYINLIKRMKQIEDKIEEIESKQKKIENEIARIKKIKLVPRGSLEWSHPQFEK > > > ================================================================================ > Running cycle 1 of predict_and_build > > ================================================================================ > Not using any supplied msas > No supplied templates will be used in prediction this cycle > > > ================================================================================ > Predicting models for 0 chains with alphafold > > Updating chain names in model list... > Chain A: > MKLCILLAVVAFVGLSLGRSLASVSTGYRLTTFEPYTPMLVNDSVQSVDGLYEMQIPTNFTIGHHEEFIQTRSPKVTIDCAAFVCGDNTACRQQLVEYGSFCVNVNAILNEVNNLLDNMQLQVASALMQGVTISSRLPDGISGPIDDINFSPLLGCIGSTCAEDGNGPSAIRGRSAIEDLLFDKVKLSDVGFVEAYNNCTGGQEVRDLLCVQSFNGIKVLPPVLSESQISGYTTGATAAAMFPPWSAAAGVPFSLSVQYRINGLGVTMNVLSENQKMIASAFNNALGAIQDGFDATNSALGKIQSVVNANAEALNNLLNQLSNRFGAISASLQEILTRLEAVEAKAQIDRLINGRLTALNAYISKQLSDSTLIKVSAAQAIEKVNECVKSQTTRINFCGNGNHILSLVQNAPYGLYFIHFSYVPISFTTANVSPGLCISGDRGLAPKAGYFVQDDGEWKFTGSSYYYPEPITDKNSVIMSSCAVNYTKAPEVFLNTSIPNPPDFKEELDKWFKNQTSIAPDLSLDFEKLNVTLLDLTYEMNRIQDAIKKLNESYINLIKRMKQIEDKIEEIESKQKKIENEIARIKKIKLVPRGSLEWSHPQFEK > Total of 1 working models > Total MSAs obtained: 0 > > Updating chain IDs > Previous ID: 'A' New ID: 'A' > MODEL: af2_group_0.pdb > > Getting processed (trimmed, B-values updated) models > B-value field interpreted as pLDDT (0 - 100) > Maximum rmsd of 1.50 A used > Maximum B-value to be included: 59.22 A**2 > Removing short segments: (chain A and resseq 537:539) > Total of 492 of 605 residues kept after B-factor filtering > > Selection string for B-factor filtering: (chain A and resseq 15:20) or > (chain A and resseq 25:136) or (chain A and resseq 145:157) or (chain A > and resseq 174:200) or (chain A and resseq 207:494) or (chain A and > resseq 541:586) > > Selecting domains as compact chains > Clusters: 15 Threshold: 3.90 > Clusters: 5 Threshold: 4.40 > Clusters: 6 Threshold: 4.82 > Clusters: 5 Threshold: 4.34 > Clusters: 3 Threshold: 3.27 > Clusters: 2 Threshold: 2.14 > Clusters: 3 Threshold: 3.98 > Clusters: 2 Threshold: 1.81 > Clusters: 3 Threshold: 3.74 > Clusters: 2 Threshold: 1.80 > Best resolution for domains is 35.0 A giving 3 regions > > Selection list based on domains: > (resseq 15:20) or (resseq 25:136) or (resseq 145:157) or (resseq 174:200) > or (resseq 207:494) or (resseq 541:586) (492 residues) > Total of 1 regions identified > Obtained processed model from af2_group_0.pdb with 492 residues (of 605) > =============================================================================== > > Finished with prediction (Job PredictAndBuild_0 cycle 1 at 2025-01-01 > 20:56:19) > =============================================================================== > > > =============================================================================== > > Getting scaffold model... (Job PredictAndBuild_0 cycle 1 at 2025-01-01 > 20:56:19) > =============================================================================== > > > > Checking whether scaffold model is complete... > > > > ================================================================================ > Getting new scaffold model in > /data2/xukui/data/jobs_pab/6b3o/PredictAndBuild_0_CarryOn/PredictAndBuild_0_scaffold_cycle_1.pdb > > ================================================================================ > > > ================================================================================ > Docking 1 models (to represent 3 sequences) in map to create a scaffold > > > ================================================================================ > Model to dock: af2_group_0.pdb: > MKLCILLAVVAFVGLSLGRSLASVSTGYRLTTFEPYTPMLVNDSVQSVDGLYEMQIPTNFTIGHHEEFIQTRSPKVTIDCAAFVCGDNTACRQQLVEYGSFCVNVNAILNEVNNLLDNMQLQVASALMQGVTISSRLPDGISGPIDDINFSPLLGCIGSTCAEDGNGPSAIRGRSAIEDLLFDKVKLSDVGFVEAYNNCTGGQEVRDLLCVQSFNGIKVLPPVLSESQISGYTTGATAAAMFPPWSAAAGVPFSLSVQYRINGLGVTMNVLSENQKMIASAFNNALGAIQDGFDATNSALGKIQSVVNANAEALNNLLNQLSNRFGAISASLQEILTRLEAVEAKAQIDRLINGRLTALNAYISKQLSDSTLIKVSAAQAIEKVNECVKSQTTRINFCGNGNHILSLVQNAPYGLYFIHFSYVPISFTTANVSPGLCISGDRGLAPKAGYFVQDDGEWKFTGSSYYYPEPITDKNSVIMSSCAVNYTKAPEVFLNTSIPNPPDFKEELDKWFKNQTSIAPDLSLDFEKLNVTLLDLTYEMNRIQDAIKKLNESYINLIKRMKQIEDKIEEIESKQKKIENEIARIKKIKLVPRGSLEWSHPQFEK > Calculating how many copies of each sequence > Model: A > MKLCILLAVVAFVGLSLGRSLASVSTGYRLTTFEPYTPMLVNDSVQSVDGLYEMQIPTNFTIGHHEEFIQTRSPKVTIDCAAFVCGDNTACRQQLVEYGSFCVNVNAILNEVNNLLDNMQLQVASALMQGVTISSRLPDGISGPIDDINFSPLLGCIGSTCAEDGNGPSAIRGRSAIEDLLFDKVKLSDVGFVEAYNNCTGGQEVRDLLCVQSFNGIKVLPPVLSESQISGYTTGATAAAMFPPWSAAAGVPFSLSVQYRINGLGVTMNVLSENQKMIASAFNNALGAIQDGFDATNSALGKIQSVVNANAEALNNLLNQLSNRFGAISASLQEILTRLEAVEAKAQIDRLINGRLTALNAYISKQLSDSTLIKVSAAQAIEKVNECVKSQTTRINFCGNGNHILSLVQNAPYGLYFIHFSYVPISFTTANVSPGLCISGDRGLAPKAGYFVQDDGEWKFTGSSYYYPEPITDKNSVIMSSCAVNYTKAPEVFLNTSIPNPPDFKEELDKWFKNQTSIAPDLSLDFEKLNVTLLDLTYEMNRIQDAIKKLNESYINLIKRMKQIEDKIEEIESKQKKIENEIARIKKIKLVPRGSLEWSHPQFEK > Model copies: 1 Sequence copies: 3 > Remainder copies: > {'MKLCILLAVVAFVGLSLGRSLASVSTGYRLTTFEPYTPMLVNDSVQSVDGLYEMQIPTNFTIGHHEEFIQTRSPKVTIDCAAFVCGDNTACRQQLVEYGSFCVNVNAILNEVNNLLDNMQLQVASALMQGVTISSRLPDGISGPIDDINFSPLLGCIGSTCAEDGNGPSAIRGRSAIEDLLFDKVKLSDVGFVEAYNNCTGGQEVRDLLCVQSFNGIKVLPPVLSESQISGYTTGATAAAMFPPWSAAAGVPFSLSVQYRINGLGVTMNVLSENQKMIASAFNNALGAIQDGFDATNSALGKIQSVVNANAEALNNLLNQLSNRFGAISASLQEILTRLEAVEAKAQIDRLINGRLTALNAYISKQLSDSTLIKVSAAQAIEKVNECVKSQTTRINFCGNGNHILSLVQNAPYGLYFIHFSYVPISFTTANVSPGLCISGDRGLAPKAGYFVQDDGEWKFTGSSYYYPEPITDKNSVIMSSCAVNYTKAPEVFLNTSIPNPPDFKEELDKWFKNQTSIAPDLSLDFEKLNVTLLDLTYEMNRIQDAIKKLNESYINLIKRMKQIEDKIEEIESKQKKIENEIARIKKIKLVPRGSLEWSHPQFEK': > 0} remainder: 0 > Copies to use: 3 > Setting up model for dock_and_rebuild > Added model af2_group_0.pdb (A) for dock_and_rebuild > > Running dock_and_rebuild to dock models > > Total of 1 predicted models > MODEL: > MKLCILLAVVAFVGLSLGRSLASVSTGYRLTTFEPYTPMLVNDSVQSVDGLYEMQIPTNFTIGHHEEFIQTRSPKVTIDCAAFVCGDNTACRQQLVEYGSFCVNVNAILNEVNNLLDNMQLQVASALMQGVTISSRLPDGISGPIDDINFSPLLGCIGSTCAEDGNGPSAIRGRSAIEDLLFDKVKLSDVGFVEAYNNCTGGQEVRDLLCVQSFNGIKVLPPVLSESQISGYTTGATAAAMFPPWSAAAGVPFSLSVQYRINGLGVTMNVLSENQKMIASAFNNALGAIQDGFDATNSALGKIQSVVNANAEALNNLLNQLSNRFGAISASLQEILTRLEAVEAKAQIDRLINGRLTALNAYISKQLSDSTLIKVSAAQAIEKVNECVKSQTTRINFCGNGNHILSLVQNAPYGLYFIHFSYVPISFTTANVSPGLCISGDRGLAPKAGYFVQDDGEWKFTGSSYYYPEPITDKNSVIMSSCAVNYTKAPEVFLNTSIPNPPDFKEELDKWFKNQTSIAPDLSLDFEKLNVTLLDLTYEMNRIQDAIKKLNESYINLIKRMKQIEDKIEEIESKQKKIENEIARIKKIKLVPRGSLEWSHPQFEK > > > ================================================================================ > Running dock_and_rebuild on total of 3 chains > Chain 1 (chain A from af2_group_0.pdb) > Chain 2 (chain A from af2_group_0.pdb) > Chain 3 (chain A from af2_group_0.pdb) > > ================================================================================ > > > ================================================================================ > Running on chain 1 (chain A from af2_group_0.pdb) > > ================================================================================ > Working directory for this chain: > PredictAndBuild_0/local_dock_and_rebuild_1_0 > No docked model for chain A ... > Running search... > > Running standard docking... > > =============================================================================== > > Processing input model > =============================================================================== > > > B-value field interpreted as pLDDT (0 - 100) > Maximum rmsd of 1.50 A used > Maximum B-value to be included: 59.22 A**2 > Removing short segments: (chain A and resseq 537:539) > Total of 492 of 605 residues kept after B-factor filtering > > Selection string for B-factor filtering: (chain A and resseq 15:20) or > (chain A and resseq 25:136) or (chain A and resseq 145:157) or (chain A > and resseq 174:200) or (chain A and resseq 207:494) or (chain A and > resseq 541:586) > > Selecting domains as compact chains > Clusters: 15 Threshold: 3.90 > Clusters: 5 Threshold: 4.40 > Clusters: 6 Threshold: 4.82 > Clusters: 5 Threshold: 4.34 > Clusters: 3 Threshold: 3.27 > Clusters: 2 Threshold: 2.14 > Clusters: 3 Threshold: 3.98 > Clusters: 2 Threshold: 1.81 > Clusters: 3 Threshold: 3.74 > Clusters: 2 Threshold: 1.80 > Best resolution for domains is 35.0 A giving 3 regions > > Selection list based on domains: > (resseq 15:20) or (resseq 25:136) or (resseq 145:157) or (resseq 174:200) > or (resseq 207:494) or (resseq 541:586) (492 residues) > Total of 1 regions identified > Obtained processed model with 492 residues (of 605) > Wrote processed model to > /data2/xukui/data/jobs_pab/6b3o/PredictAndBuild_0/local_dock_and_rebuild_1_0/working_model_processed.pdb > > =============================================================================== > > Extracting unique part of map > =============================================================================== > > > > Setting map-model-manager and model shift to zero during run > Split model into chains: A1 > Chain number: 1 id: A1 Residues: 492 > > ============================================================================== > > Searching with each chain as a seed > ============================================================================== > > > > ============================================================================== > > Running dock-in map on domain A1 with 492 residues > ============================================================================== > > > > Running dock-in-map at overall resolution of 4.1 A > Density radius set to: 24.6 A > Placing model in map > > Map has been not been offset > New cell after running map_box: (435.20, 424.32, 435.20, 90.00, 90.00, > 90.00) > Target boxes set to 20 > > Choosing local part of search model to use in search... > > Shifting search model coordinates (0.3, 1.9, -1.9) to origin > and creating search map coefficients > > Docking with MR... > Using masked map data > MODEL: full_shifted_sm_1.pdb mass: 54120 (copies: 1) > Estimated solvent fraction: 0.95 > Total atoms in all copies: 3781 (volume = 66567.6 A**3) > Solvent fraction (as used) is about 0.94 > Total good sites: 11268 > Max clusters: 1 > Wrote mtz data to > PredictAndBuild_0/local_dock_and_rebuild_1_0/run_mr/mtz_data.mtz > Wrote model A1_full_shifted_sm_1.pdb to > PredictAndBuild_0/local_dock_and_rebuild_1_0/run_mr/A1_full_shifted_sm_1.pdb > Wrote model A_from_cluster_0.pdb to > PredictAndBuild_0/local_dock_and_rebuild_1_0/run_mr/A_from_cluster_0.pdb > _______________________________________________ > 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 > -- Thomas C Terwilliger Laboratory Fellow, Los Alamos National Laboratory Senior Scientist, New Mexico Consortium 100 Entrada Dr, Los Alamos, NM 87544 Email: tterwilliger(a)newmexicoconsortium.org Tel: 505-431-0010

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Error phenix refine with ligands
by miriam.cavinato＠unimi.it 07 Jan '25

07 Jan '25

Hi everyone, I am trying to refine my model containing a ligand (a thiophene -like molecule with a 7 carbon atom cycle attached). I create restraints with ready set utility or directly with eLBOW, then I use phenix.refine and I get this error: "fatal problems in interpreting model file: number of atoms with unknown nonbonded energy type symbols: 12 Please edit the model file to resolve the problems or/and supply a CIF file with matching restraint definitions, along with apply_cif_modification and apply_cif_link parameter definition if necessary". Another problem is that as soon as I try to open REEL or open any result to check restraints, Phenix crashes... I was wondering if someone has the same issue and can help me figure it out! Thanks in advance Best regards Miriam

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