- phenixbb - phenix-online.org

Cis/trans peptide plane restraints ?
by CUNIASSE Philippe 13 Sep '23

13 Sep '23

Dear all, I am currently trying to refine a MDFF structure with the phenix RealSpaceRefine protocol of phenix. I am wondering if it is possible to apply systematic restraints to peptide plane (in trans when they are trans and cis when they are cis in order to avoid twisted conformations of the peptide planes at the end of the refinement. The only possibility I saw is to apply dihedral restraints defined one by one but when having thousands of residues, it seems not really convenient. Thanks in advance for your help. Best regards. Philippe. ----------------------------------------------- Philippe Cuniasse, PhD/HDR. Institut de Biologie Integrative de la cellule. UMR 9198 CNRS-CEA-Univ Paris Sud Bat 144 CE-Saclay 91191 Gif-sur-Yvette Cedex France Tel: (33) 1 69 08 56 35 Fax: (33) 1 69 08 47 12 Email: philippe.cuniasse(a)cea.fr<mailto:[email protected]> Web: http://biodev.cea.fr/rasmot3d/ [signature_863913621][signature_2053578832][signature_1816548304] -----------------------------------------------

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Re: [phenixbb] Command line phenix.sculpt_ensemble
by Randy John Read 11 Sep '23

11 Sep '23

Dear Matthew, Sorry, I somehow missed this for a few days. The first thing I would say is that I’m not sure there’s much of a use case for sculptor and ensembler (or the combined application you were using) in these days of AlphaFold. Sculpted ensembles were a really powerful way to combine information from a collection of distant homologues to make a better model for molecular replacement. However, since AlphaFold became available I think the current best approach in this scenario is to take the AlphaFold model (which will integrate everything known structurally about the class of proteins far better than ensembler), run it through process_predicted_model (to downweight or trim off the less reliable parts of the model) and use that single model as your molecular replacement model. I haven’t yet seen a counter-example where the experimental structures of the distant homologues are better. Of course, if someone has a counter-example that would be very interesting to learn about! In terms of this bug, I’m wondering whether it’s a Python compatibility issue. I’m guessing that your Mac might be one of the newer ones with ARM (M1 or M2) chips. If so, are you using a build for the older Intel processors, or the native ARM build? In any case, if you’re using the ARM build then this will be built with Python 3. The easiest way to tell is to go to a terminal window with Phenix set up and type: phenix.python --version This will report whether or not you’re using Python 2.7 or Python 3.7. The sculpt_ensemble procedure has a lot of options, and I would need to know exactly which options you had set in order to try to reproduce the problem. Could you look in the project directory for a file with a name like .phenix/project_data/sculpt_ensemble_NN.eff, where “NN” is the job number? If you could send me that file, that would help. Best wishes, Randy Read > From: Whitley, Matthew (NIH/NCI) [C] <matthew.whitley(a)nih.gov> > Date: Thu, Sep 7, 2023 at 10:54 PM > Subject: [phenixbb] Command line phenix.sculpt_ensemble > To: phenixbb(a)phenix-online.org <phenixbb(a)phenix-online.org> > > > Hello all, > I am trying to use the command line tool phenix.sculpt_ensemble to process a series of PDB files in preparation for molecular replacement. > However, when I run the following on the command line: > phenix.sculpt_ensemble 2*.pdb input.target_sequence=RRAS2.fasta > I get the following errors: > Traceback (most recent call last): > File "/Applications/phenix-1.21rc1-5015/build/../modules/phaser/phaser/command_line/sculpt_ensemble.py", line 84, in <module> > sculpt_ensemble.run( phil = params.phil, logger = logger ) > File "/Applications/phenix-1.21rc1-5015/modules/phaser/phaser/sculpt_ensemble.py", line 610, in run > logger = logger, > File "/Applications/phenix-1.21rc1-5015/modules/phaser/phaser/sculpt_ensemble.py", line 259, in read_in_target_sequence_files > for ( fname, i ) in itertools.zip_longest( filenames, range( 1, nchains + 1 ) ): > AttributeError: 'module' object has no attribute 'zip_longest' > I am running phenix 1.21rc1-5015-000 on Mac OS 13.5.1. > Any ideas? > Thanks, > Matthew > _______________________________________________ > phenixbb mailing list > phenixbb(a)phenix-online.org > http://phenix-online.org/mailman/listinfo/phenixbb > Unsubscribe: phenixbb-leave(a)phenix-online.org ----- Randy J. Read Department of Haematology, University of Cambridge Cambridge Institute for Medical Research Tel: +44 1223 336500 The Keith Peters Building Hills Road E-mail: rjr27(a)cam.ac.uk Cambridge CB2 0XY, U.K. www-structmed.cimr.cam.ac.uk

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Command line phenix.sculpt_ensemble
by Whitley, Matthew (NIH/NCI) [C] 07 Sep '23

07 Sep '23

Hello all, I am trying to use the command line tool phenix.sculpt_ensemble to process a series of PDB files in preparation for molecular replacement. However, when I run the following on the command line: phenix.sculpt_ensemble 2*.pdb input.target_sequence=RRAS2.fasta I get the following errors: Traceback (most recent call last): File "/Applications/phenix-1.21rc1-5015/build/../modules/phaser/phaser/command_line/sculpt_ensemble.py", line 84, in <module> sculpt_ensemble.run( phil = params.phil, logger = logger ) File "/Applications/phenix-1.21rc1-5015/modules/phaser/phaser/sculpt_ensemble.py", line 610, in run logger = logger, File "/Applications/phenix-1.21rc1-5015/modules/phaser/phaser/sculpt_ensemble.py", line 259, in read_in_target_sequence_files for ( fname, i ) in itertools.zip_longest( filenames, range( 1, nchains + 1 ) ): AttributeError: 'module' object has no attribute 'zip_longest' I am running phenix 1.21rc1-5015-000 on Mac OS 13.5.1. Any ideas? Thanks, Matthew

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Phenix presentation at IUCr Melbourne Software Fayre
by Dorothee Liebschner 25 Aug '23

25 Aug '23

Hi everyone, For those of you attending the IUCr conference in Melbourne, please note the following presentations at the Software Fayre. Talks in the Software Fayre are unfortunately not listed in the conference app, so I advertise it here. "Phenix - Macromolecular structure determination using crystallographic and cryo-EM data" (*Dorothee Liebschner*) When: Saturday, 8/26, 12:45 - 13:30pm Where: Room 214 Topics include: - Introduction to Phenix - What's new - Using predicted models for Crystallography "Physics-based macromolecular model building with ISOLDE" (*Tristan Croll*) When: Saturday, 8/26, 14:15 - 15:00 pm Where: Room 214 Best wishes, Dorothee -- Research Scientist, Molecular Biophysics and Integrated Bioimaging Lawrence Berkeley National Laboratory 1 Cyclotron Road, M/S 33R0345 Berkeley, CA 94720 Tel: (510) 486-5709 Fax: (510) 486-5909 Web: https://phenix-online.org

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Generation of residual electron density maps using IAS (inter atomic scatteres) model
by Ankur Kumar Singh 08 Aug '23

08 Aug '23

Dear Members, I am working on a protein structure resolved at 1.1 angstroms, and I am trying to generate a residual electron density map. I am following a series of articles from Prof. Afonine (Macromolecular refinement at subatomic resolution with interatomic scatterers<https://pubmed.ncbi.nlm.nih.gov/18007035/>). Here, an IAS modeling of the protein structure is done, followed by refinement in Phenix. The residual density is observed in conventional maps. I am trying to figure out how to create an IAS model for my protein structure. Please suggest any relevant method/article to obtain the model. And also, is it possible to have an IAS model for a protein resolved at 1.1 angstroms? Many thanks for considering my request. ----- Regards, Ankur K Singh Graduate Student

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General interest: Data matters session at the ACA 2023 in Baltimore
by John R Helliwell 05 Aug '23

05 Aug '23

Dear Colleagues, I have placed a note about this at the IUCr Committee on Data Public Forum: https://forums.iucr.org/viewtopic.php?f=39&t=457&sid=54ca94b6a4db968acc28ab… including a weblink to my slides at Zenodo. Best wishes, John Emeritus Professor John R Helliwell DSc

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[URGENT] Sorry: Fatal problems interpreting PDB file
by Esra A 02 Aug '23

02 Aug '23

Hello everyone, I am Esra Ayan. I would like to ask you about getting an error in Phenix: *Sorry: Fatal problems interpreting PDB file* *I followed the below command to resolve this issue:* 1. just running "phenix.ready_set MR.1.pdb" 2. then running "phenix.refine MR.1.updated.pdb MR.1.mtz MR.1.ligands.cif refinement.input.xray_data.r_free_flags.generate=True This way, i was able to solve the problem but still getting high Rwork and Rfree values. I still couldn't lower the values even though I tried many ways. What is your recommendation about this issue? i was wondering if I did a mistake by using Step 1 and Step 2 commands. You can find the reference pdb and mtz files in the attachment. Any help would be appreciated. Kind regards, Esra Ayan

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Postdoctoral position in drug discovery
by Harp, Joel M 02 Aug '23

02 Aug '23

Postdoctoral position in drug discovery An opening is available in the drug discovery laboratory of Dr. Stephen Fesik for a post-doc in the field of protein x-ray crystallography. Responsibilities will include protein production, fragment screening by NMR, and all aspects of x-ray crystallography including preparation of protein-ligand complexes, crystallization, home/synchrotron data collection, and structure determination. Additional experience in molecular biology including construct design, cloning, site-directed mutagenesis and modeling is a plus. The ideal candidate should be self-motivated and be able to communicate efficiently in a highly collaborative environment. Please send cv to jason.phan(a)Vanderbilt.Edu<mailto:[email protected]> The Vanderbilt campus is located in Nashville Tennessee. Also known as Music City, Nashville is a fast growing and dynamic environment with plenty of cultural attractions and opportunities for outdoor recreation.

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High Temperature Factors with TLS
by Thomas, Leonard M. 02 Aug '23

02 Aug '23

Hello All, A general questions though phenix.refine is being used for refinement. A student I am working with has a structure that was solved and initially refined using TLS and NCS parameters. They were given the structure to gain some experience in refinement and they have been asking me some questions, I was not involved in the initial work. While everything seems to be happy and the model is correct with good refinement statistics for the most part one thing that I am unsure of is some of the heavier atoms (Phosphate and Sulfer) have very high temperature factors when looking at individual residues or ligands. The temperature factors are at least twice as high as the lighter atoms they are associated with. I am at a loss to explain what is going on, I really have not used TLS refinement a lot so there is that. Resolution is about 2.5 angstroms with good completeness. Thoughts? Thank You in advance Len Thomas Leonard Thomas, Ph.D. Biomolecular Structure Core, Director Oklahoma COBRE in Structural Biology Price Family Foundation Institute of Structural Biology University of Oklahoma Department of Chemistry and Biochemistry 101 Stephenson Parkway Norman, OK 73019-5251 Office: (405)325-1126 lmthomas(a)ou.edu<mailto:[email protected]> http://www.ou.edu/structuralbiology/cobre-core-facilities/mcl

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Job Advert: Drug Discovery Project Research Scientist position, Francis Crick Institute, London, UK.
by David Briggs 01 Aug '23

01 Aug '23

Dear all, We have a position available at the Francis Crick Institute - please share with any soon-to-finish PhD students and postdocs who might be interested: We seek a talented, highly motivated and independent post-doctoral project research scientist to work on a project to design protein kinase C beta selective inhibitors for B cell malignancies. Work will be carried out in Neil McDonald's laboratory at the Francis Crick Institute, in collaboration with clinician-scientist Ingo Ringshausen at the University of Cambridge, and is funded by a Cancer Research Horizon Therapeutic Catalyst Award. The project will be funded for 18 months in the first instance, with the potential for extension depending on progress. The project will build upon prior work within our laboratory to characterise and develop new, selective kinase inhibitors. The work will involve both optimisation of existing inhibitors, and the parallel discovery of novel inhibitors using an XChem Fragment screening approach at Diamond Light Source. The Francis Crick Institute is situated in central London, and is the largest single-site biomedical research institute in Europe, with excellent provision for X-ray crystallography and medicinal chemistry to allow rapid characterisation and follow-up of any lead compounds. Prior experience with baculovirus protein expression and X-ray crystallography would be advantageous. Informal enquiries can be made to Professor Neil McDonald (neil.mcdonald(a)crick.ac.uk). Application Deadline: 1st Sept 2023. For more details about the role and the application process, please see: https://crick.wd3.myworkdayjobs.com/External/job/London/Postdoctoral-Projec… -- Dr David C. Briggs CSci MRSB (he/him) Principal Laboratory Research Scientist Signalling and Structural Biology Lab The Francis Crick Institute London, UK Working hours: Mon-Fri 0900-1700 == about.me/david_briggs<https://about.me/david_briggs> | OrcID<https://orcid.org/0000-0002-9793-7339> | Google Scholar <https://scholar.google.co.uk/citations?user=DRKG5KwAAAAJ> The Francis Crick Institute Limited is a registered charity in England and Wales no. 1140062 and a company registered in England and Wales no. 06885462, with its registered office at 1 Midland Road London NW1 1AT

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