- phenixbb - phenix-online.org

racemic ligand refinement
by Calvin N Steussy 15 Sep '23

15 Sep '23

All, I need to refine a ligand that consists of two stereoisomers in my active site. I have decent density and have created models for the r and s forms of the guest with separate cif files. They have been fit independently into the active site density. My questions are; How to show these in the pdb file. Separate chains? Separate amino acids in a given chain? How do I keep them from interacting with one another during refinement? Creating an alt-position seems obvious but I'm not certain how to apply the different stereo restraints in that case. I'm sure someone has solved this before but I can't seem to find that information. Thanks, Nic Steussy Purdue University.

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Phenix workshop at 80th Pittsburgh Diffraction Conference (October 14, 2023)
by Pavel Afonine 14 Sep '23

14 Sep '23

Dear community, this is a reminder that we will be hosting a Phenix user workshop at 80th Pittsburgh Diffraction Conference on October 14, 2023 and there are still spaces available! https://web.cvent.com/event/03acbdbf-b2ae-4875-a16f-672346cf1fd1/summary This is a great opportunity to learn about latest and greatest features of Phenix, ask questions and seek expert advice on your specific problems. See you all there! All the best, Pavel

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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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