- phenixbb - phenix-online.org

Recommendations for refining a large model against many focused maps
by Vorländer,Matthias Kopano 02 Oct '23

02 Oct '23

Hi everyone, Apologies if this has been asked before, but I would like to know what are the recommended procedures to refine a model against many (>10) cryo-EM maps from local refinement? Some of the maps have substantial overlap between them, and I manually annotated which part of the model is best resolved in which map. Very grateful for any suggestions, Best wishes, Matthias

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exploding refinement
by Daniel Larsson 26 Sep '23

26 Sep '23

Hi developers, I'm having difficulty minimizing ribosome structures using real_space_refine. The structures are mostly fine (I think) and there are no sever close-contacts. But it seems to happen in particular with waters and/or hydrogens present. See below for an example error message. Searching the mailing list archive, I found an old thread on the same topic where Pavel explained that this can happen when the weights are set improperly. https://phenix-online.org/pipermail/phenixbb/2017-November/023588.html I suspect my problems are related to the ad hoc method of setting weights does not work well for a large structure with 150,000+ atoms. When I check the log file, the weight estimation looks like this: XYZ refinement ************** Weight determination summary: number of chunks: 2038 random chunks: chunk 1215 optimal weight: 50.0000 chunk 784 optimal weight: 5.9990 chunk 1173 optimal weight: 50.0000 chunk 591 optimal weight: 30.0000 chunk 385 optimal weight: 50.0000 chunk 380 optimal weight: 2.9990 chunk 1248 optimal weight: 50.0000 chunk 1338 optimal weight: 50.0000 chunk 971 optimal weight: 50.0000 chunk 183 optimal weight: 50.0000 chunk 1543 optimal weight: 50.0000 overall best weight: 27.7996 So there seems to be a large discrepancy for the optimal weight for different chunks. Out of a 10-macro cycle run (crashed on the last cycle), the overall best weight varied between 3.7 and 34, which I suspect contributes to the unstable minimization procedure. overall best weight: 33.9998 overall best weight: 20.5996 overall best weight: 5.0186 overall best weight: 4.6388 overall best weight: 3.7586 overall best weight: 34.1998 overall best weight: 27.7996 overall best weight: 18.1996 overall best weight: 9.1992 Do you think a constant weight could be a solution to this problem? Is it possible to set it manually? Which of the weights are set using the heuristic method? Are there different weights for e.g. bonded restraints and "extra" metal bond restraints? There are some references to weights in the .eff file and nonbonded_weight seems to be an interesting option with a default value of 100. Regards, Daniel Example run that explodes: phenix.real_space_refine resolution=2 run=minimization_global nproc=4 output.prefix=phe output.suffix=_min ignore_symmetry_conflicts=True macro_cycles=10 ligands.cif elbow.edits coot-42.pdb map.mrc Traceback (most recent call last): File "/Applications/phenix-1.20.1-4487/build/../modules/phenix/phenix/command_line/real_space_refine.py", line 8, in <module> run_program(real_space_refine.Program) File "/Applications/phenix-1.20.1-4487/modules/cctbx_project/iotbx/cli_parser.py", line 79, in run_program task.run() File "/Applications/phenix-1.20.1-4487/modules/phenix/phenix/programs/real_space_refine.py", line 207, in run log = self.logger) File "/Applications/phenix-1.20.1-4487/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 297, in __init__ self.caller(self.refine_xyz) File "/Applications/phenix-1.20.1-4487/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 312, in caller func() File "/Applications/phenix-1.20.1-4487/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 653, in refine_xyz self.minimization_no_ncs() File "/Applications/phenix-1.20.1-4487/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 716, in minimization_no_ncs log = self.log) File "/Applications/phenix-1.20.1-4487/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 51, in __init__ gradients_method = gradients_method) File "/Applications/phenix-1.20.1-4487/modules/cctbx_project/mmtbx/refinement/real_space/weight.py", line 87, in __init__ rms_angles_limit = rms_angles_limit) File "/Applications/phenix-1.20.1-4487/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 368, in refine rms_angles_limit = rms_angles_limit) File "/Applications/phenix-1.20.1-4487/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/Applications/phenix-1.20.1-4487/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 112, in refine states_collector = self.states_accumulator) File "/Applications/phenix-1.20.1-4487/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 174, in __init__ exception_handling_params=lbfgs_exception_handling_params) File "/Applications/phenix-1.20.1-4487/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/Applications/phenix-1.20.1-4487/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/Applications/phenix-1.20.1-4487/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 245, in compute_functional_and_gradients compute_gradients=True) File "/Applications/phenix-1.20.1-4487/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1479, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/Applications/phenix-1.20.1-4487/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1381, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/Applications/phenix-1.20.1-4487/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1262, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 58.8204 > 50: distance: 19 - 25: 20.675 distance: 21 - 22: 4.594 distance: 21 - 23: 14.720 distance: 22 - 24: 27.218 distance: 25 - 26: 15.535 distance: 25 - 138: 20.583 distance: 26 - 27: 10.976 distance: 26 - 29: 9.260 distance: 27 - 28: 6.472 distance: 27 - 34: 28.251 distance: 28 - 135: 26.553 distance: 29 - 30: 30.275 distance: 30 - 31: 45.594 distance: 31 - 32: 42.003 distance: 32 - 33: 58.820 distance: 34 - 35: 15.118 distance: 34 - 40: 32.473 distance: 35 - 36: 10.126 distance: 35 - 38: 33.272 distance: 36 - 37: 36.153 distance: 36 - 41: 14.653 distance: 38 - 39: 31.110 distance: 39 - 40: 31.467 distance: 41 - 42: 36.418 distance: 42 - 43: 13.145 distance: 43 - 44: 8.206 distance: 43 - 45: 40.869 distance: 45 - 46: 12.390 distance: 46 - 47: 25.848 distance: 46 - 49: 16.457 distance: 47 - 48: 15.264 distance: 47 - 53: 38.374 distance: 49 - 50: 27.548 distance: 50 - 51: 46.020 distance: 50 - 52: 31.107 distance: 53 - 54: 25.030 distance: 54 - 55: 33.266 distance: 55 - 56: 15.731 distance: 55 - 57: 17.553 distance: 57 - 58: 8.147 distance: 58 - 59: 15.533 distance: 58 - 61: 3.968 distance: 59 - 60: 32.012 distance: 59 - 66: 13.102 distance: 60 - 143: 27.836 distance: 61 - 62: 21.904 distance: 62 - 63: 22.068 distance: 63 - 64: 40.044 distance: 64 - 65: 14.241 distance: 66 - 67: 13.162 distance: 67 - 68: 14.727 distance: 67 - 70: 18.482 distance: 68 - 69: 7.119 distance: 68 - 74: 16.874 distance: 70 - 71: 23.617 distance: 70 - 72: 26.751 distance: 71 - 73: 31.237 distance: 74 - 75: 24.016 distance: 74 - 146: 23.850 distance: 75 - 76: 10.199 distance: 75 - 78: 26.004 distance: 76 - 77: 12.111 distance: 76 - 81: 13.195 distance: 77 - 157: 10.604 distance: 78 - 79: 24.115 distance: 78 - 80: 26.622 distance: 81 - 82: 9.528 distance: 82 - 83: 10.254 distance: 82 - 85: 9.660 När du har kontakt med oss på Uppsala universitet med e-post så innebär det att vi behandlar dina personuppgifter. För att läsa mer om hur vi gör det kan du läsa här: http://www.uu.se/om-uu/dataskydd-personuppgifter/ E-mailing Uppsala University means that we will process your personal data. For more information on how this is performed, please read here: http://www.uu.se/en/about-uu/data-protection-policy

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Updating other tools to use and output in mmCIF format and option to add hydrogens in real_space_refine
by Adrián González López 21 Sep '23

21 Sep '23

Hi Phenix team, I have a couple of feature suggestions: It would be great if all the other tools within phenix would be able to have mmCIF files as both input and output. It causes a lot of problems when you are forced to switch between pdb and mmCIF, for example when using ReadySet to add hydrogens. On that note, it would also be very useful to have an option in real space refine to add hydrogens automatically before the refinement and remove them after the refinement. Thanks! Best, Adrián När du har kontakt med oss på Uppsala universitet med e-post så innebär det att vi behandlar dina personuppgifter. För att läsa mer om hur vi gör det kan du läsa här: http://www.uu.se/om-uu/dataskydd-personuppgifter/ E-mailing Uppsala University means that we will process your personal data. For more information on how this is performed, please read here: http://www.uu.se/en/about-uu/data-protection-policy

3 2

map deposition strategy after density modification
by Daniel Larsson 20 Sep '23

20 Sep '23

Hi Phenix community, I’ve been using density modification with some success for my data and am considering the most appropriate way to do model building/refinement and then deposition of my results. Here are some questions/observations: 1) Which map should I refine against (most importantly, do the final minimization using phenix.real_space_refine)? The DM map is the most clear one, so I’m favoring to do it against this one (as long as the geometry/validation is also best for this one). 2) Which map should I deposit as my main map? Is it the autosharpened one or the DM one? Since the DM map looks the best, I want the user who only downloads one map to see this one, so again I favoring this map. 3) Which nominal resolution should I quote for my reconstruction? Since the procedure seems to introduce correlation between the two maps (see point 4 below), it does not seem to be possible to obtain a gold-standard FSC value between two truly independent half-maps. As the DM procedure supposedly actually improves the map (by leveraging knowledge about what solvent and macromolecular maps usually looks like and thereby improves the Fourier coefficients), it feels like it would be misrepresenting the data by quoting the FSC_0.143 from the original reconstruction. Should I use the FSC_0.5 estimated value that phenix.resolve_cryo_em outputs? 4) Which FSC curve should I deposit? When I calculate the FSC between the two density modified half-maps, I get a funny (or rather not so funny) looking curve with a bump at around 3Å and it does not go to zero at Nyquist (which does not agree with the map quality). This must again be due to the induced correlation between the maps, presumably during the masking of solvent and macromolecule density. Phenix.resolve_cryo_em calculates a FSC curve to calculate the FSC_0.5 value, which according to the manual page corrects for the correlation induced between the two maps: "Density modification introduces some correlations between half-maps due to solvent flattening. This can have a small effect on the resolution estimates obtained with half-map FSC. The resolution estimates provided by the program are corrected for this effect." But is this curve good enough? I think OneDeposit wants to have the gold-standard FSC curve, right? 5) Which (nowadays mandatory) half-maps should one deposit? Here I would say that the original half-maps before DM makes more sense, since these are less processed. But if one specify these as the half-maps, there will be inconsistencies during validation, since the DM map will look quite different from the average between the two original half-maps. Also the automatic FSC curve will be very different from the deposited one. So in conclusion, despite what I say above, the most conservative thing would be to deposit the conventionally sharpened map as my main map and use the original half-maps for calculating the FSC-curve and use the 0.143 threshold from this curve to estimate the resolution. The DM map can be used during rebuilding/refinement, but I think final minimization should be against the main map during deposition (with restraints if the geometry gets worse). The DM map can be deposited as an auxiliary map. Do the community and the developers agree? Regards, Daniel När du har kontakt med oss på Uppsala universitet med e-post så innebär det att vi behandlar dina personuppgifter. För att läsa mer om hur vi gör det kan du läsa här: http://www.uu.se/om-uu/dataskydd-personuppgifter/ E-mailing Uppsala University means that we will process your personal data. For more information on how this is performed, please read here: http://www.uu.se/en/about-uu/data-protection-policy

4 4

autogenerate restraint.eff from PDB for phenix.varref
by vincent Chaptal 18 Sep '23

18 Sep '23

Hi Phenix team, Before launching phenix.varref, I would like to generate a ligand restraint file so the ligand doesn't fly away from its density. It would be great if the ligand_restraints.eff file could be generated from a PDB file already containing the ligand (for example originating from refinement), that we can then edit afterwards. The ligand I'm talking about is ATP in this case, so it doesn't need external cif file for refinement. I searched but couldn't identify such a job. It would be useful if it could be added to "PDB tools" or similar. Thank Best Vincent -- Vincent Chaptal, PhD Director of GdR APPICOM Drug Resistance and Membrane Proteins Lab MMSB -UMR5086 7 passage du Vercors 69007 LYON FRANCE +33 4 37 65 29 01 http://www.appicom.cnrs.fr http://mmsb.cnrs.fr/en/

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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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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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latest nightly build that runs on windows flawless
by Georg Mlynek 31 Jul '23

31 Jul '23

Hi community members, what is the latest latest nightly build that runs on windows flawless? I tried several versions after dev 4815 in the last year but all of them had different bugs. Most importantly the import of old projects should work. Many thanks, br Georg.

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General interest
by John R Helliwell 17 Jul '23

17 Jul '23

Dear Colleagues, I imagine that this book on the History of Scientific Journals: Publishing at The Royal Society 1665-2015, which I have reviewed in the current issue of J Appl Cryst will be of interest:- https://journals.iucr.org/j/issues/2023/04/00/xo0198/index.html My review is open access. The book itself is also open access:- https://www.jstor.org/stable/j.ctv2gz3zp1 Best wishes, John Emeritus Professor John R Helliwell DSc

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Phenix Phaser Question
by hyun4867 11 Jul '23

11 Jul '23

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

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symmetry finding question
by Dmitry Semchonok 06 Jul '23

06 Jul '23

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

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Discrepancy between Phenix GUI and command line for MR
by Xavier Brazzolotto 04 Jul '23

04 Jul '23

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

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General interest, education article
by John R Helliwell 04 Jul '23

04 Jul '23

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Young Crystallographers Meeting in Strasbourg
by Triantafyllidis, Dimitrios P. 29 Jun '23

29 Jun '23

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

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Apply NFC operators to get identical 14 homo oligomeric model
by Dmitry Semchonok 28 Jun '23

28 Jun '23

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

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