- phenixbb - phenix-online.org

phenix.refine command line: what to change on the subsequent def file to point to the desired input pdb
by Alejandro Buschiazzo 02 Aug '24

02 Aug '24

Dear phenix users/developers Some time ago there were several modifications on the names/specifications of important parameters/options (such as miller_array for structure factor files, etc) Running phenix.refine by command lines (no gui) is my favorite, and I am now running into several difficulties: 1- what’s the difference between miller_array and default_miller_array; or model and default_model? 2- what’s the precise definition of phil_files and default_phil? What to change if I manually edit my .eff? 3- how should I use the new automatically created .def file for subsequent refinement cycles after I’ve manually rebuilt (I need to point to the new pdb input file: I usually screw this up, can’t seem to use the newly created .def as my starting instructions file anymore, it complains that I have problems in the right definition of the input pdb, or too many models...) 4- I often fall into a loop where by default newly created .eff files include a dry_run=true option (e.g. when I deliberately tell phenix.refine to overwrite previous .eff files) Thanks a lot for clarifying on these issues: and sorry, for I couldn’t find obvious answers to them in the documentation (probably my fault!!) Also, I am using phenix v 1.21.1-5286 (on a Sonoma MacOS laptop) With best wishes Alejandro

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Reminder: Macromolecular Crystallography - CSHL Course October 2024
by Paul Adams 30 Jul '24

30 Jul '24

Dear Colleagues, We have extended the deadline for the course applications to August 9th. A reminder that the Cold Spring Harbor Macromolecular Crystallography course will take place October 13-29th this year (pleased see below for more details). This comprehensive course is an outstanding place to learn both the theoretical and practical aspects of macromolecular crystallography. There are extensive lectures and practical sessions from world recognized experts in crystallization, data collection, data processing, structure solution, refinement, and validation. The goal of the course is for researchers who have had some exposure to structural biology to become experts in crystallography. This is an experience in macromolecular crystallography learning that cannot be found anywhere else, and the student/teacher ratio is often 1:1. Please follow the link below to the course web site. In particular, please note the information about the various fellowships, scholarships, and stipends that are available. If anyone has any questions please send me an e-mail, and we will be happy to answer all queries. Paul Adams Cold Spring Harbor Laboratory - Meetings & Courses | 1 Bungtown Road, Cold Spring Harbor, NY 11724 -- 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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Instruct-ERIC Workshop on “Sample Preparation for Single Particle Analysis by Cryo-Electron Microscopy”
by Jose Artur Brito 24 Jul '24

24 Jul '24

Dear Colleagues, We hereby announce a 4-day workshop on "Sample Preparation for Single Particle Analysis by Cryo-Electron Microscopy" [1 [1]]. The course is funded by Instruct-ERIC and will be held at the Iberian Nanotechnology Laboratory (Braga, Portugal), between the 7th and 10th of October this year. The Workshop is aimed primarily at Ph.D students and young Post-Doctoral researchers, is set to provide in-depth training on sample preparation for single particle analysis (SPA) by cryo-electron microscopy (cryo-EM), and is hosted by a team of experts from ITQB NOVA [2 [2]], INL [3 [3]], CNB-CSIC [4 [4]], i3S [5 [5]], and SciLifeLab [6 [6]]. Participants will engage in a comprehensive course featuring a blend of lectures and hands-on tutorials. The lectures will delve into the principles of SPA, covering theoretical and practical aspects of preparing biological samples for negative staining, quality assessment and data collection. The workshop will highlight recent advancements in protein production and stabilization, as well as the latest technological innovations in grid preparation and sample manipulation. Attendees are encouraged to bring their samples, providing a unique opportunity to apply newly acquired skills to their specific research needs. Practical sessions will offer hands-on experience with vitrification using a plunge-freezing device and optimizing grids for sample screening with a cryo-transmission electron microscope (TEM). Participants will be limited to 12 to allow a closer interaction between the participants and the tutors. Candidate selection will be based on a short CV, a motivation letter from the Applicant, and a recommendation letter from the Supervisor. Registration deadline is August 19, 2024, and can be done at the following link: https://www.events.inl.int/instruct-eric-workshop Registration fee is 250Eur for Academics and 500Eur for Non-Academic, and includes accommodation, lunches, coffee-breaks and social dinner. Please feel free to contact us if you have any question. On behalf of the organizing team, hoping to see you in Braga, Jose Artur Brito - ITQB NOVA [1] https://instruct-eric.org/events/16th-instruct-eric-hands-on-workshop-sampl… [2] https://www.itqb.unl.pt/ [3] https://www.inl.int/ [4] http://www.cnb.csic.es/index.php/en [5] https://www.i3s.up.pt/ [6] https://www.scilifelab.se/ -- Links: ------ [1] https://instruct-eric.org/events/16th-instruct-eric-hands-on-workshop-sampl… [2] https://www.itqb.unl.pt/ [3] https://www.inl.int/ [4] http://www.cnb.csic.es/index.php/en [5] https://www.i3s.up.pt/ [6] https://www.scilifelab.se/

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AutoBuild trouble
by Atsushi Nakagawa 17 Jul '24

17 Jul '24

Dear all, I cannot run AutoBuild from GUI both on dev-5383 and 1.21.1. The process terminated with the following message during the process of AutoBuild_multiple_models. Job terminated with at new message window shown below, ********************************************************************************* Failed to carry out AutoBuild_multiple_models: ‘module’ object has no attribute ‘run_autobuild’ ********************************************************************************* Is there any problem on my installation or parameters? AutoBuild runs with the older version (1.20). Thank you for your help. Atsushi

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running phenix
by khkim＠korea.ac.kr 16 Jul '24

16 Jul '24

Dear colleagues, Running phenix received an error (below). Status window indicates "You appear to have another session of PHENIX running already (hostname...), which has locked your project database". I had tried to change project directories. Many thanks. Error in sys.excepthook: Traceback (most recent call last): File "/usr/local/bin/phenix-1.20.1-4487/modules/phenix/wxGUI2/App.py", line 898, in _excepthook Error.show_exception_dialog(type, value, traceback) File "/usr/local/bin/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 "/usr/local/bin/phenix-1.20.1-4487/build/../modules/phenix/wxGUI2/command_line/main.py", line 23, in <module> run(sys.argv[1:]) File "/usr/local/bin/phenix-1.20.1-4487/build/../modules/phenix/wxGUI2/command_line/main.py", line 17, in run wxapp = App.PhenixApp(args) File "/usr/local/bin/phenix-1.20.1-4487/modules/phenix/wxGUI2/App.py", line 74, in __init__ wx.App.__init__(self, 0) File "/usr/local/bin/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 "/usr/local/bin/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 "/usr/local/bin/phenix-1.20.1-4487/modules/phenix/wxGUI2/App.py", line 120, in OnInit self.start_gui() File "/usr/local/bin/phenix-1.20.1-4487/modules/phenix/wxGUI2/App.py", line 191, in start_gui self.launch_main() File "/usr/local/bin/phenix-1.20.1-4487/modules/phenix/wxGUI2/App.py", line 507, in launch_main frame = PhenixGUI() File "/usr/local/bin/phenix-1.20.1-4487/modules/phenix/wxGUI2/Home/Main.py", line 51, in __init__ self.setup_panels() File "/usr/local/bin/phenix-1.20.1-4487/modules/phenix/wxGUI2/Home/Main.py", line 171, in setup_panels self.refresh_project_list() File "/usr/local/bin/phenix-1.20.1-4487/modules/phenix/wxGUI2/Home/Main.py", line 360, in refresh_project_list self.add_projects(group_name=current_group) File "/usr/local/bin/phenix-1.20.1-4487/modules/phenix/wxGUI2/Home/Main.py", line 352, in add_projects group_name=group_name) File "/usr/local/bin/phenix-1.20.1-4487/modules/phenix/phenix/tracking/project_db.py", line 72, in get_project_summaries group_id = self.get_group_id_by_name(to_unicode(group_name)) File "/usr/local/bin/phenix-1.20.1-4487/modules/phenix/phenix/tracking/project_db.py", line 608, in get_group_id_by_name assert (name in [None, "None", "All", "All groups"]) AssertionError

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Re: [phenixbb] C-beta outliers - it is 1.20 version issue
by Andrea Smith 13 Jul '24

13 Jul '24

Thank you everyone for suggestions. As it turns out, there is a problem in the 1.20 phenix version that I was using. I updated to 1.21 as suggested by Dorothee, repeated one refinement job and had no more C-beta outliers, so I am guessing I will not have them in other models either. Best, Andrea On Friday, June 14, 2024 21:16 CEST, Nigel Moriarty <nwmoriarty(a)lbl.gov> wrote: Andrea Can you send me files off-line? Cheers Nigel ---Nigel W. Moriarty Building 33R0349, Molecular Biophysics and Integrated BioimagingLawrence Berkeley National Laboratory Berkeley, CA 94720-8235 Email : NWMoriarty(a)LBL.govWeb : CCI.LBL.govORCID : orcid.org/0000-0001-8857-9464 On Thu, Jun 13, 2024 at 9:59 AM Andrea Smith <andrea.smith(a)uochb.cas.cz> wrote: Hi all, I am running Phenix v. 1.20.1-4487 on Windows and I keep on getting C-beta outliers of methionine residues after phenix.refine (happened in different data from two different proteins). Even if I correct the methionines in Coot (and they fit perfectly in the density), I get the outliers at the end of refinement again (while these outliers don't fit the density and I can see a green difference map where the C-beta is). Why is this? Is there a way to tell phenix.refine not to move a specific amino acid during refinement? Thanks, Andrea _______________________________________________ phenixbb mailing list phenixbb(a)phenix-online.org http://phenix-online.org/mailman/listinfo/phenixbb Unsubscribe: phenixbb-leave(a)phenix-online.org

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refine and Table 1
by Andrea Smith 09 Jul '24

09 Jul '24

Hi everyone, * I have an issue with phenix.refine being unable to open generated pdb and mtz files in coot after refinement. It claims “ERROR: refinement output file not found!” This started happening after I opened the model in ChimeraX and used dssp command and then saved model as pdb that I used for further refinements. The files generated from phenix.refine actually exist, but instead of just being named e.g. myprotein_refine20.pdb they are called myprotein_refine19_refine020.pdb (yes there is an extra refine and an extra 0). This has never happened to me before. * I am also trying to generate "Table 1" for journal. I input my pdb into model file and mtz into reflection file. When I click Run, I get an error message: "a model is referenced in the phil which is not in the data manager". What does this mean? * I also tried to validate my model using pdb validate server, but when I upload cif files generated as output from phenix.refine, the server shows “Error processing uploaded files…Click to reload”. (However, when I use the Get PDB validation report task in phenix, I get a validation report pdf with no issues.) Is all of this caused by the changes the ChimeraX's dssp command did to my pdb? Thank you, Andrea Running Phenix 1.21-5207 from GUI on Ubuntu 20.04.3.

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Re: [phenixbb] refine and Table 1
by Andrea Smith 09 Jul '24

09 Jul '24

Hi Yi Min, my problem number 2 was indeed resolved after I restarted my system. Thank you, Andrea On Tuesday, July 09, 2024 14:47 CEST, Yi Min Ng <yimin_ng(a)outlook.com> wrote: Hi Andrea, I am still new to this field and I have previously came across your #2 problem when trying to generate Table 1 using Phenix. I don't know exactly what was causing the problem but I somehow managed to generate Table 1 after restarting the GUI. You might want to try restarting the software if you haven't tried so? Hope some experts will be able to help you with the problems soon 🤞 Best wishes,Yi Min ______________________________________________________________________________ From: phenixbb-bounces(a)phenix-online.org <phenixbb-bounces(a)phenix-online.org> on behalf of Andrea Smith <andrea.smith(a)uochb.cas.cz> Sent: 09 July 2024 14:25 To: phenixbb(a)phenix-online.org <phenixbb(a)phenix-online.org> Subject: [phenixbb] refine and Table 1 Hi everyone, * I have an issue with phenix.refine being unable to open generated pdb and mtz files in coot after refinement. It claims “ERROR: refinement output file not found!” This started happening after I opened the model in ChimeraX and used dssp command and then saved model as pdb that I used for further refinements. The files generated from phenix.refine actually exist, but instead of just being named e.g. myprotein_refine20.pdb they are called myprotein_refine19_refine020.pdb (yes there is an extra refine and an extra 0). This has never happened to me before. * I am also trying to generate "Table 1" for journal. I input my pdb into model file and mtz into reflection file. When I click Run, I get an error message: "a model is referenced in the phil which is not in the data manager". What does this mean? * I also tried to validate my model using pdb validate server, but when I upload cif files generated as output from phenix.refine, the server shows “Error processing uploaded files…Click to reload”. (However, when I use the Get PDB validation report task in phenix, I get a validation report pdf with no issues.) Is all of this caused by the changes the ChimeraX's dssp command did to my pdb? Thank you, Andrea Running Phenix 1.21-5207 from GUI on Ubuntu 20.04.3.

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Computations Crystallography Newsletter (CCN) Submissions
by Nigel Moriarty 01 Jul '24

01 Jul '24

Folks The deadline for submissions to the Computational Crystallography Newsletter (CCN) is 22 JAN 2024. Please consider writing an article of general interest to the community. The Computational Crystallography Newsletter (CCN) is an electronic newsletter for structural biologists, and is published online every 6 months. Feature articles, meeting announcements and reports can be submitted to me at any time for consideration. Submission of text by email or word-processing files using the CCN templates is requested. Cheers Nigel --- Nigel W. Moriarty Building 33R0349, Molecular Biophysics and Integrated Bioimaging Lawrence Berkeley National Laboratory Berkeley, CA 94720-8235 Email : NWMoriarty(a)LBL.gov Web : CCI.LBL.gov ORCID : orcid.org/0000-0001-8857-9464

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real_space_refine is un-glycosylating my protein
by robert＠oeffner.net 01 Jul '24

01 Jul '24

Hi, I am trying to do a refinement with phenix.real_space_refine (RSR) on an EM map with a protein and a known ligand (NAG is the monomer code). In the pdb file supplied the C1 atom in the NAG molecule is positioned nicely in the EM density at a distance of 1.38Å from a ND2 atom in an ASN residue of the protein. The O1 atom in the NAG molecule is not present suggesting there should be a covalent bond here I believe. Both ASN and the NAG molecule have the same chainID. The problem is that RSR moves the sugar away even though I have used command line options such as pdb_interpretation.automatic_linking.link_carbohydrates=True or even pdb_interpretation.automatic_linking.link_all=True. The atoms end up at an un-bonded distance of 2.85Å from each other after refinement to the point that one of them is poking out of the density. Are my phil parameters incorrect? I noticed that I don't get an error message if I misspell say pdb_interpretation.automatic_linking.link_carbohydrates to pdb_interpretation.automatic_linking.link_carbohydrate. RSR still runs to completion so I'm wondering if it actually interprets the PHIL parameter at all. Another peculiarity is that the log file comments that NAG is an unusual residue rather than stating it is a well-known carbohydrate. If anyone on here knows how to compel phenix RSR into creating automatic links to carbohydrates suggestions would be much appreciated. Many thanks, Rob

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