- phenixbb - phenix-online.org

convergence in Phenix real space refinement
by Robert Oeffner 21 Oct '23

21 Oct '23

Hi, I'm curious to know when convergence has been obtained in phenix_real_space_refine. I see the number "moved from start" in the log file and assume that once it doesn't change much after several macro cycles then convergence has been obtained when refining a structure. True? What is that value based on, the RMSD between the initial structure and the final structure? I didn't find this documented in the 2018 publication of the program. Many thanks, Rob

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Renumbering while retaining refinement info
by Patrick Loll 16 Oct '23

16 Oct '23

Hello all, I've finished refining a handful of related structures, but now I need to renumber the residues to reflect the fact that I’m working with a truncated construct (like a dope I didn’t do this at the outset). However, when I run PDB Tools, it does not write the refinement information into the output CIF. Is there a way to get around this, other than re-running the final cycle of refinement with the renumbered coordinates (or entering the refinement info by hand? This would be easy in the PDB format, but not so much in mmCIF). Cheers, Pat __________________________________ Patrick J. Loll, PhD (he, him, his) Professor of Biochemistry & Molecular Biology Drexel University College of Medicine Room 10-102 New College Building 245 N. 15th St. Philadelphia, PA 19102-1192 USA (267) 359-2653 pjl28(a)drexel.edu

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reflection file editor - only 1 dataset#
by vincent Chaptal 11 Oct '23

11 Oct '23

Hi, I have a reflection file generated by phenix.refine, which contains HKL, I, Rfree, SIGI, Fs..., Fmodel... and map coeffs. All these arrays are placed in several dataset#. I would like to place them all in a single Dataset#. Is it possible to do that using the reflection file editor? I've tried to modify the output with "edit arrays" but I can't figure out how to do that? Thank you. 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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Last week to apply for tenure track Data-driven life sciences fellowships
by Nicholas Pearce 10 Oct '23

10 Oct '23

Hi all, If you're interested in starting your own research group in data-driven life sciences, it's currently the last week for applications for positions available all over Sweden in multiple disciplines (including structural biology!). Each recruitment package has a budget of 17 MSEK to cover salary for 5 years as DDLS Fellow, two PhD positions and two postdoc positions, as well as running costs. Most of the Fellow positions are tenure-track, and the respective hosting universities/organizations take long-term responsibility of tenured group leaders. More information here: https://www.scilifelab.se/data-driven/fellows/ Feel free to email if you have any questions! Thanks, Nick ——— Nicholas Pearce Assistant Professor in Bioinformatics SciLifeLab | Data-Driven Life Sciences (DDLS) Fellow Linköping University Sweden

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Phenix installation on macOS 14 Sonoma
by Kizziah, James 06 Oct '23

06 Oct '23

Hi all, I am having trouble getting Phenix to open on a new mac. I downloaded the latest official release of the point-and-click installer, ran xattr -c on it, and installed without issue. Initially, I can create the first project directory (or recreate it if I remove the .phenix directory), but then I get a notice that another instance of Phenix is running with the associated PID. If I continue anyway, python quits unexpectedly, and if Phenix is opened in the command line, this reply is given: “python[9678:116756] It's not legal to call -layoutSubtreeIfNeeded on a view which is already being laid out. If you are implementing the view's -layout method, you can call -[super layout] instead. Break on void _NSDetectedLayoutRecursion(void) to debug. This will be logged only once. This may break in the future. [3] segmentation fault phenix” However, the PID for this supposed other instance doesn’t exist. This occurs every time Phenix is run from Applications or in the command line, even after restarting the laptop (without resuming programs) or deleting and reinstalling Phenix. Any ideas how to solve this problem? Thanks, James

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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 27 Sep '23

27 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 22 Sep '23

22 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

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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

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autogenerate restraint.eff from PDB for phenix.varref
by vincent Chaptal 19 Sep '23

19 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 16 Sep '23

16 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 15 Sep '23

15 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] 08 Sep '23

08 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 03 Aug '23

03 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 03 Aug '23

03 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.

1 0

High Temperature Factors with TLS
by Thomas, Leonard M. 03 Aug '23

03 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

2 1

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

1 0

latest nightly build that runs on windows flawless
by Georg Mlynek 01 Aug '23

01 Aug '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.

2 1

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

1 0

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

2 1

symmetry finding question
by Dmitry Semchonok 07 Jul '23

07 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

3 2

Discrepancy between Phenix GUI and command line for MR
by Xavier Brazzolotto 05 Jul '23

05 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

3 9

General interest, education article
by John R Helliwell 05 Jul '23

05 Jul '23

2 1

Young Crystallographers Meeting in Strasbourg
by Triantafyllidis, Dimitrios P. 30 Jun '23

30 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

1 0

Apply NFC operators to get identical 14 homo oligomeric model
by Dmitry Semchonok 29 Jun '23

29 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

2 1

Postdoctoral position in method development (York Structural Biology Laboratory)
by Jon Agirre 27 Jun '23

27 Jun '23

Dear all, Applications are invited for a Postdoctoral Research Associate position, funded by the Royal Society, for up to 30 months to work with Dr Jon Agirre in the Department of Chemistry. The successful applicant will join a vibrant team of researchers at the heart of the world-leading York Structural Biology Laboratory (YSBL). The work of the laboratory over the years has included the delivery of world-leading methods and experimental discoveries, training and nurturing hundreds of outstanding scientists in the process. Role The AlphaFold software for protein model prediction has revolutionised workflows in structural biology. However, while high-accuracy models are now available for most human proteins of medical relevance, up to 50% of those proteins are expected to be glycosylated – a modification whose structure AlphaFold does not predict. Protein glycosylation is greatly important, with implications for protein folding and molecular recognition including, as evidenced by the spike glycoprotein of SARS-CoV-2, viral infection. In collaboration with other scientists, we have extended the Privateer software to interactively build missing glycosylation onto precalculated AlphaFold models. In parallel, we have developed analyses that allow us to get a clear picture of glycans and their interactions, including H-bonds and XH-Pi interactions. We expect that these methods will enable us to, based on existing glycobiological knowledge, extend the Privateer software to automatically complete AlphaFold models with crucial missing glycosylation components. We are seeking a person with an interest in both biology and coding, who can collaborate with others in a very diverse team with a mission to further our knowledge of glycobiology and seize the opportunities presented by a deeper understanding of it. Main duties and responsibilities To develop and extend the Privateer software to complete AlphaFold models with the missing glycan components. To further our existing collaborations with CCP4, CCP-EM, PDB-REDO, the Protein Data Bank and the AlphaFold Protein Structure Database. Department The Department of Chemistry is one of the largest and most successful departments at York and we are renowned internationally for our research. As a department, we strive to provide a working environment that allows all staff and students to contribute fully, to flourish, and to excel. We are proud of our Athena Swan Gold Award. The Department of Chemistry values all employees for the qualities and skills they bring to the workplace and aims to be a diverse and egalitarian community in which all can thrive. For informal enquiries: please contact Dr Jon Agirre, jon.agirre(a)york.ac.uk To apply: https://jobs.york.ac.uk/vacancy/research-associate-529961.html Deadline for applications: 20 August 2023. Many thanks for making it this far in the advert! With best wishes, Jon -- Dr Jon Agirre Royal Society University Research Fellow (assistant professor) CCP4 WG2 co-chair | instruct-ERIC representative @ 3D-Bioinfo SC (Elixir) York Structural Biology Laboratory, Department of Chemistry University of York, Heslington, YO10 5DD, York, UK

1 0

problems in running Phenix
by Gianluca Cioci 27 Jun '23

27 Jun '23

Dear All, I am experiencing difficulties in installing Phenix in my Linux system based on Ubuntu 20.04.6 LTS (GNU/Linux 5.15.0-75-generic x86_64) Installation is completed, but when I try tu run phenix I get the message: 12:57:27: Cannot set locale to language "English". 12:57:27: locale 'en_GB' cannot be set. and in the terminal I get: Error in sys.excepthook: Traceback (most recent call last): File "/data/software/phenix/phenix-1.20.1-4487/modules/phenix/wxGUI2/App.py", line 898, in _excepthook Error.show_exception_dialog(type, value, traceback) File "/data/software/phenix/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 "/data/software/phenix/phenix-1.20.1-4487/build/../modules/phenix/wxGUI2/command_line/main.py", line 23, in <module> run(sys.argv[1:]) File "/data/software/phenix/phenix-1.20.1-4487/build/../modules/phenix/wxGUI2/command_line/main.py", line 17, in run wxapp = App.PhenixApp(args) File "/data/software/phenix/phenix-1.20.1-4487/modules/phenix/wxGUI2/App.py", line 74, in __init__ wx.App.__init__(self, 0) File "/data/software/phenix/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 "/data/software/phenix/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 "/data/software/phenix/phenix-1.20.1-4487/modules/phenix/wxGUI2/App.py", line 108, in OnInit show_splash_screen(timeout=2000) File "/data/software/phenix/phenix-1.20.1-4487/modules/phenix/wxGUI2/App.py", line 952, in show_splash_screen dlg,-1,citations.format_citation(citations.citations_db.get("phenix"))) File "/data/software/phenix/phenix-1.20.1-4487/conda_base/lib/python2.7/site-packages/wx-3.0-gtk2/wx/_controls.py", line 997, in __init__ _controls_.StaticText_swiginit(self,_controls_.new_StaticText(*args, **kwargs)) UnicodeDecodeError: 'ascii' codec can't decode byte 0xc3 in position 40: ordinal not in range(128) Anyone has a working solution for this ? We have tried to change the locale to en_GB, but still it's not working. With many thanks, GIA -- Dr. Gianluca CIOCI Toulouse Biotechnology Institute (TBI) https://www.toulouse-biotechnology-institute.fr/en/poles/equipe-cimes/ PICT - Plateforme Intégrée de Criblage de Toulouse http://www.pict.ipbs.fr/ Tel: +33 (0)5 61 55 97 68 E-mail: cioci(a)insa-toulouse.fr TBI - INSA Toulouse 135 avenue de Rangueil 31077 Toulouse CEDEX 04 http://www.toulouse-biotechnology-institute.fr

2 1

Refining peptides with beta-amino acids
by Bram Mylemans 27 Jun '23

27 Jun '23

Dear experts, I’m trying to refine a crystal structure of a peptide that contains some beta-amino acids. I have tried generating restraints with elbow from a sdf file. I changed the naming of the atoms to conform with the protein naming and added the L-peptide linking tag. This seems to work for refining and also local refine in coot works. However, the peptide bond is not kept planar. Does anyone have an idea how to make sure the amide bond is correctly constrained? I have included the restrained file I made for L-beta-Leucine below for reference. Best wishes, ---------- Dr. Bram Mylemans Post-doctoral Research Associate Woolfson group School of Chemistry University of Bristol # electronic Ligand Builder and Optimisation Workbench (eLBOW) # - a module of PHENIX version 1.20.1-4487- # - file written: Sun May 14 14:31:25 2023 # # Inital geometry file: a 60 line input string # Ligand name: (3S)-3-amino-5-methylhexanoic acid # Quantum optimisation: True # Method: uhf # Random seed: 3628800 # SMILES string: CC(C)C[C@H](N)CC(O)=O # data_comp_list loop_ _chem_comp.id _chem_comp.three_letter_code _chem_comp.name _chem_comp.group _chem_comp.number_atoms_all _chem_comp.number_atoms_nh _chem_comp.desc_level B3L B3L '(3S)-3-amino-5-methylhexanoic acid' L-peptide 24 10 . # data_comp_B3L # loop_ _chem_comp_atom.comp_id _chem_comp_atom.atom_id _chem_comp_atom.type_symbol _chem_comp_atom.type_energy _chem_comp_atom.charge _chem_comp_atom.partial_charge _chem_comp_atom.x _chem_comp_atom.y _chem_comp_atom.z B3L O O O 0 -0.621 -0.0468 -0.0672 0.0379 B3L C C C 0 0.403 1.2030 -0.0409 -0.0524 B3L CA C CH2 0 -0.215 2.0004 0.0099 1.2717 B3L CB C CH1 0 0.109 1.5936 -1.1463 2.1941 B3L N N NH2 0 -0.452 2.4198 -2.3233 1.9111 B3L CG C CH2 0 -0.173 1.7636 -0.6462 3.6485 B3L CD C CH1 0 -0.040 1.5804 -1.7407 4.6994 B3L CE2 C CH3 0 -0.160 1.9937 -1.1916 6.0651 B3L CE1 C CH3 0 -0.159 0.1402 -2.2497 4.7124 B3L HA H HCH2 0 0.055 3.0941 0.0115 1.0876 B3L HAA H HCH2 0 0.036 1.7870 0.9871 1.7352 B3L HB H HCH1 0 0.088 0.5145 -1.4120 2.0199 B3L HN H HNH2 0 0.153 1.9179 -3.1939 1.9355 B3L HG H HCH2 0 0.049 2.7650 -0.1815 3.7540 B3L HGA H HCH2 0 0.063 1.0542 0.1844 3.8432 B3L HD H HCH1 0 0.048 2.2575 -2.6020 4.4708 B3L H3E2 H HCH3 0 0.033 2.4606 -1.9617 6.6915 B3L H2E2 H HCH3 0 0.049 2.7302 -0.3796 5.9910 B3L H1E2 H HCH3 0 0.045 1.1543 -0.7788 6.6358 B3L H3E1 H HCH3 0 0.045 0.0304 -3.1957 4.1675 B3L H2E1 H HCH3 0 0.034 -0.2410 -2.4354 5.7240 B3L H1E1 H HCH3 0 0.068 -0.5687 -1.5528 4.2450 B3L OXT O OC -1 -0.606 1.8564 -0.0003 -1.1279 B3L HNA H HNH2 0 0.147 3.2587 -2.3840 2.4671 # loop_ _chem_comp_bond.comp_id _chem_comp_bond.atom_id_1 _chem_comp_bond.atom_id_2 _chem_comp_bond.type _chem_comp_bond.value_dist _chem_comp_bond.value_dist_esd B3L C O single 1.253 0.015 B3L C OXT single 1.259 0.016 B3L CA C single 1.546 0.037 B3L CB CA single 1.534 0.036 B3L CB HB single 1.125 0.040 B3L N CB single 1.466 0.036 B3L N HNA single 1.008 0.037 B3L CG CB single 1.547 0.037 B3L CG HG single 1.109 0.039 B3L CD CG single 1.528 0.035 B3L CD CE1 single 1.528 0.035 B3L CE2 CD single 1.529 0.035 B3L CE2 H1E2 single 1.096 0.038 B3L CE1 H1E1 single 1.098 0.038 B3L CE1 H3E1 single 1.097 0.038 B3L HA CA single 1.109 0.037 B3L HAA CA single 1.102 0.040 B3L HN N single 1.005 0.037 B3L HGA CG single 1.110 0.039 B3L HD CD single 1.119 0.040 B3L H3E2 CE2 single 1.097 0.038 B3L H2E2 CE2 single 1.099 0.038 B3L H2E1 CE1 single 1.097 0.038 # loop_ _chem_comp_angle.comp_id _chem_comp_angle.atom_id_1 _chem_comp_angle.atom_id_2 _chem_comp_angle.atom_id_3 _chem_comp_angle.value_angle _chem_comp_angle.value_angle_esd B3L OXT C CA 117.56 2.401 B3L CA C O 116.95 2.270 B3L OXT C O 125.42 1.837 B3L HAA CA HA 105.03 2.935 B3L HAA CA CB 111.34 2.722 B3L HA CA CB 111.25 2.583 B3L HAA CA C 106.82 2.670 B3L HA CA C 111.50 2.415 B3L CB CA C 110.69 2.417 B3L HB CB CG 109.11 2.657 B3L CG CB N 112.27 2.657 B3L HB CB N 108.74 2.657 B3L CG CB CA 107.01 2.247 B3L N CB CA 109.86 2.386 B3L HB CB CA 109.83 2.388 B3L HNA N HN 110.49 3.000 B3L HN N CB 114.17 2.677 B3L HNA N CB 114.27 2.682 B3L HGA CG HG 104.29 2.953 B3L HGA CG CD 109.80 2.649 B3L HG CG CD 110.06 1.813 B3L HGA CG CB 109.67 2.659 B3L CD CG CB 113.69 2.657 B3L HG CG CB 108.91 2.671 B3L HD CD CE1 108.40 2.672 B3L HD CD CE2 107.17 2.674 B3L CE1 CD CE2 111.53 2.389 B3L HD CD CG 109.76 2.723 B3L CE2 CD CG 108.95 2.259 B3L CE1 CD CG 110.95 2.656 B3L H1E2 CE2 H2E2 105.67 2.934 B3L H2E2 CE2 H3E2 105.78 2.934 B3L H1E2 CE2 H3E2 107.05 2.933 B3L H2E2 CE2 CD 112.73 2.662 B3L H3E2 CE2 CD 111.91 2.665 B3L H1E2 CE2 CD 113.17 2.686 B3L H1E1 CE1 H2E1 106.00 2.935 B3L H2E1 CE1 H3E1 106.10 2.936 B3L H1E1 CE1 H3E1 105.73 2.935 B3L H2E1 CE1 CD 113.07 2.437 B3L H3E1 CE1 CD 112.17 2.708 B3L H1E1 CE1 CD 113.17 2.649 # loop_ _chem_comp_tor.comp_id _chem_comp_tor.id _chem_comp_tor.atom_id_1 _chem_comp_tor.atom_id_2 _chem_comp_tor.atom_id_3 _chem_comp_tor.atom_id_4 _chem_comp_tor.value_angle _chem_comp_tor.value_angle_esd _chem_comp_tor.period B3L Var_01 CB CA C O 54.55 30.0 2 B3L Var_02 CE1 CD CG CB -66.07 30.0 1 B3L Var_03 H1E1 CE1 CD CG -19.34 30.0 3 B3L Var_04 H1E2 CE2 CD CG 93.46 30.0 3 # loop_ _chem_comp_chir.comp_id _chem_comp_chir.id _chem_comp_chir.atom_id_centre _chem_comp_chir.atom_id_1 _chem_comp_chir.atom_id_2 _chem_comp_chir.atom_id_3 _chem_comp_chir.volume_sign B3L chir_01 CB CA N CG negativ # loop_ _chem_comp_plane_atom.comp_id _chem_comp_plane_atom.plane_id _chem_comp_plane_atom.atom_id _chem_comp_plane_atom.dist_esd B3L plan-1 O 0.020 B3L plan-1 C 0.020 B3L plan-1 CA 0.020 B3L plan-1 OXT 0.020

2 1

phenix.model_idealization
by Manoj saxena 21 Jun '23

21 Jun '23

Hi , I am trying to fix a pdb file that was obtained from Rosetta and has some distorted helices so I trier to fix that with > phenix.model_idealization model.pdb use_ss_restraints = True I am attaching the log file , here is the end of the log file. Any suggestions on what's going on ? " NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Traceback (most recent call last): File "/Applications/phenix-1.20.1-4487/build/../modules/cctbx_project/mmtbx/command_line/model_idealization.py", line 1118, in <module> run(sys.argv[1:]) File "/Applications/phenix-1.20.1-4487/build/../modules/cctbx_project/mmtbx/command_line/model_idealization.py", line 1106, in run mi_object.run() File "/Applications/phenix-1.20.1-4487/build/../modules/cctbx_project/mmtbx/command_line/model_idealization.py", line 548, in run self._setup_model_h() File "/Applications/phenix-1.20.1-4487/build/../modules/cctbx_project/mmtbx/command_line/model_idealization.py", line 478, in _setup_model_h params_h.pdb_interpretation = self.model._pdb_interpretation_params.pdb_interpretation AttributeError: 'NoneType' object has no attribute 'pdb_interpretation'" My aim is to idealize the secondary structure. I first tried it in Isolde but the EM density is not great and always leads to some distortion. So I was wondering if I can do this fix in Phenix. Is this model idealization tool the best approach? or I have to go in and fix things manually. Thanks Manoj

2 1

Glycosidic bonds in cif
by Engin Özkan 19 Jun '23

19 Jun '23

Hi, I am trying to deposit cif files from phenix.refine using the last stable version and the release candidate. In both, I seem many instances of C00089 covale NAG D 2012 O4 NAG AM . O4 . BMA D 2013 C1 BMA AN . C1 . 'Custom glycosidic links need to be generated when the atom names of the carbohydrates don't conform to the standard.' for every glycan-glycan bond, but 'Taken from Monomer Library or GeoStd' for ASN-NAG, which does not make sense. The log file says the ALPHA1-3, ALPHA1-6, BETA1-4 and NAG-ASN links were properly applied, but the cif only mentions NAG-ASN. The cif also includes a link definition only for NAG-ASN, but none of the other glycosidic bonds. The structures appear to have proper geometry for glycosidic bonds, so this is probably just a cif-only issue. Also, is there a way to output the cif where every glycan residue does not get a new chain (this one goes up to chain AV=48 chains)? I found at least one phenix-refined case in the PDB where one glycan chain gets a single chain ID. Admittedly, that might have been fixed post phenix.refine. Thanks, Engin -- Engin Özkan, Ph.D. Associate Professor Dept of Biochemistry and Molecular Biology University of Chicago

1 0

Two postdoc positions in Ubiquitin Signalling, WEHI, Melbourne, Australia
by Bernhard Lechtenberg 13 Jun '23

13 Jun '23

Dear colleagues, The Ubiquitin Signalling Division at The Walter and Eliza Hall Institute (WEHI) is looking to recruit two Research Officers (Postdocs) to join our teams in the Lechtenberg and Komander labs. WEHI in Melbourne is Australia’s pre-eminent medical research institute. The Ubiquitin Signalling Division at WEHI was established in 2018, and offers a vibrant, multi-disciplinary and highly collaborative environment at the forefront of ubiquitin research with access to state-of-the art facilities in proteomics, structural biology (Titan Krios G4, Australian Synchrotron), biophysics (SEC-MALS, ITC, SPR, mass photometry, MST), cell manipulation (CRISPR) and imaging facilities, and drug discovery through the National Drug Discovery Centre (NDDC). The division features a continuous stream of excellent publications, exciting preliminary data, and opportunities to establish research ideas in a multidisciplinary environment. The Lechtenberg lab seeks to recruit a postdoc with structural biology (crystallography or cryo-EM) and biochemistry expertise to study large RBR E3 ligase complexes. Preliminary data include an established mammalian expression system. Details and applications: https://wehi.wd3.myworkdayjobs.com/en-US/WEHI/job/Research-Officer---Struct… Contact: Dr. Bernhard Lechtenberg, lechtenberg.b(a)wehi.edu.au<mailto:[email protected]> The Komander lab seeks to recruit a postdoc with structural biology and protein biochemistry background to embark on an early-stage drug discovery project in the area of mitophagy and Parkinson’s disease, with excellent academic and translational / entrepreneurial outputs expected. Details and applications: https://wehi.wd3.myworkdayjobs.com/en-US/WEHI/job/Parkville-Victoria-Austra… Contact: Prof. David Komander, dk(a)wehi.edu.au<mailto:[email protected]> We offer three-year contracts with highly competitive salaries and benefits. Pre-application enquiries are encouraged via the contact details provided. Please share this information within your networks. Kind regards, Bernhard Bernhard C. Lechtenberg PhD NHMRC Emerging Leadership Fellow Laboratory Head Ubiquitin Signalling Division E lechtenberg.b(a)wehi.edu.au<mailto:[email protected]> T +61 3 9345 2217 [WEHI Logo] Walter and Eliza Hall Institute of Medical Research 1G Royal Parade Parkville Victoria 3052 Australia www.wehi.edu.au<https://wehi.edu.au> Twitter<https://twitter.com/WEHI_research> | Facebook<https://www.facebook.com/WEHIresearch/> | Instagram<https://www.instagram.com/wehi_research> | Youtube<https://www.youtube.com/user/WEHImovies> | LinkedIn<https://www.linkedin.com/company/wehi_research> WEHI acknowledges the Wurundjeri people of the Kulin Nation as the traditional owners of the land where our campuses are located and the continuing connection to country and community. Private and confidential The content of this e-mail and any attachments may be private and confidential, intended only for use of the individual or entity named. If you are not the intended recipient of this message you must not read, forward, print, copy, disclose, use or store in any way the information this e-mail or any attachment contains. If you are not the intended recipient, please notify the sender immediately and delete or destroy all copies of this e-mail and any attachment.

1 0

Issue with running phenix.segment_and_split_map command
by Das, Abhinaba 11 Jun '23

11 Jun '23

Good afternoon all, I’ve been running Phenix using the GUI however I want to segment a map using phenix.segment_and_split_map which turns out to be a command line program. I’m trying to run it using the following command: abhinabadas@AbhinabasM1Mac ~ % phenix.segment_and_split_map \ /Users/abhinabadas/Downloads/Chimera/postProcessMaskedsharpened_map.ccp4 \ /Users/abhinabadas/Desktop/Test_map_2/rcsb_pdb_3J9G.fasta auto_sharpen = False \ box_in_auto_sharpen = False However, it ends every time giving the error: Read sequence from /Users/abhinabadas/Desktop/VipA-B/rcsb_pdb_3J9G.fasta Sorry: Need resolution for segment_and_split_map with sharpening Initially, I used the same command without using auto_sharpen = False box_in_auto_sharpen = False, as the map was already auto sharpened in Phenix. It gave me the same error regardless. Apologies for this possibly inane question; there might be a very easy fix to it but I can’t seem to figure it out. I would greatly appreciate any insights or suggestions to resolve this issue. Please let me know if you need any further information. Thank you for your attention and assistance. Thanks, abhi

2 3

model symmetrisation
by Dmitry A. Semchonok 08 Jun '23

08 Jun '23

2 1

2023 Cold Spring Harbor Macromolecular Crystallography Course
by Paul Adams 05 Jun '23

05 Jun '23

Dear Colleagues, The July 15th deadline for applications to the CSHL Macromolecular Crystallography Course to be held later this year, October 15th through October 31st 2023, is rapidly approaching. This is a unique opportunity to become expert in the use of crystallography to solve challenging macromolecular structures. The official course announcement can be found here: https://meetings.cshl.edu/courses.aspx?course=C-CRYS&year=23 please pass this on to anyone who you think might be interested and would benefit, especially students and postdocs. This comprehensive course is an outstanding place to learn both the theoretical and practical aspects of macromolecular crystallography, and consists of extensive lectures and practical sessions from experts in the field. The instructor team is: Janet Newman, Tom Peat, Jim Pflugrath, Dorothee Liebschner, and myself. We are assisted by world recognized experts in crystallization, data collection, data processing, structure solution, refinement, and validation (see the course link above for more details). 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. We expect participants to crystallize one or more proteins and determine their structures in a two week period. Students may also work on their own projects, but not exclusively. They will become very well-versed in the theory of diffraction and crystal structure determination, while also having lots of fun. Both synchrotron data collection and in-house diffraction data collection will be used to solve structures. The course will also include the use of computationally predicted structures to aid in solving the crystallographic phase problem. The course is limited to 16 participants due to the very hands-on nature of the experiments and the intimate seminar and laboratory settings. Please check the above web link for more details. In particular, please note the information about the various fellowships, scholarships, and stipends that are available. The course is supported with funds provided by the National Institute of General Medical Sciences, for which we are extremely grateful. Also there are stipends available from the Leona M. and Harry B. Helmsley Charitable Trust and the Howard Hughes Medical Institute to help offset the cost of tuition. Scholarship support is also provided by Regeneron Pharmaceuticals. If anyone has any questions, please send me an e-mail, we will be happy to answer all queries. -- Paul Adams (he/him/his) Associate Laboratory Director for Biosciences, LBL (https://biosciences.lbl.gov/leadership/) Principal Investigator, Computational Crystallography Initiative, LBL (https://cci.lbl.gov) Vice President for Technology, the Joint BioEnergy Institute (http://www.jbei.org) Principal Investigator, ALS-ENABLE, Advanced Light Source (https://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 33, Room 250 Building 978, Room 4126 Building 977, Room 268 Tel: 1-510-486-4225 http://cci.lbl.gov/paul ORCID: 0000-0001-9333-8219 Lawrence Berkeley Laboratory 1 Cyclotron Road BLDG 33R0345 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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AlphaFold button
by James Holton 31 May '23

31 May '23

Maybe I'm doing it wrong, but I was trying to show a class last week how to use the AlphaFold features of phenix, only to find that the Colab seems to no longer exist? I know the dedicated server is up now, but the current stable release does not have that feature in the GUI. Will a new stable release be released soon? Just asking, -James

2 1

NCS operators
by Dmitry A. Semchonok 23 May '23

23 May '23

3 3

real space R value calculation
by heinea＠mailer.uni-marburg.de 22 May '23

22 May '23

Dear mailing list, how can I calculate real space R-values fur individual residues or regions in a protein using Phenix? Any advice would be greatly appreciated. Thank you very much in advance, Andreas

2 1

NCS operators
by Dmitry A. Semchonok 19 May '23

19 May '23

1 0

generating half maps for combined map using phenix.combine_focused_maps
by Manoj saxena 16 May '23

16 May '23

Hi all, I have a question for generating half half maps for the combined map in Phenix, I am combining 6 regions of a complex (using local refined maps) and supplying the reference map and a reference model for the complex. Additionally, I am supplying the 2 half maps for the whole complex as input fines. I was wondering if I need to supply 2 half maps for each of the local refined regions as input files in addition to the half maps for the reference map. Thank you regards Manoj

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Pb executing phenix.model_idealization
by CUNIASSE Philippe 16 May '23

16 May '23

Dear all, I tried to use the phenix.model_idealization code of phenix (in command line) following the syntax suggested inhttps://phenix-online.org/documentation/reference/model_idealization.html phenix.model_idealization xxxx.pdb But the code stops on the error : Traceback (most recent call last): File "/Applications/phenix-1.20.1-4487/build/../modules/cctbx_project/mmtbx/command_line/model_idealization.py", line 1118, in <module> run(sys.argv[1:]) File "/Applications/phenix-1.20.1-4487/build/../modules/cctbx_project/mmtbx/command_line/model_idealization.py", line 1106, in run mi_object.run() File "/Applications/phenix-1.20.1-4487/build/../modules/cctbx_project/mmtbx/command_line/model_idealization.py", line 548, in run self._setup_model_h() File "/Applications/phenix-1.20.1-4487/build/../modules/cctbx_project/mmtbx/command_line/model_idealization.py", line 478, in _setup_model_h params_h.pdb_interpretation = self.model._pdb_interpretation_params.pdb_interpretation AttributeError: 'NoneType' object has no attribute 'pdb_interpretation' Thanks in advance for any suggestion to solve this. 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_3031510868][signature_394100311][signature_2972121752] -----------------------------------------------

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How to exclude one part of a model to be taken into account during Real_Space_refinement ?
by CUNIASSE Philippe 16 May '23

16 May '23

Dear all, I am trying to do a phenix.real_space_refine in a CryoEM map at 4.2 Å with a model obtained by MDFF (NAMD, a protein DNA complex) because the resulting structure, despite a good CC and a good molecular geometry has a poor Ramachandran Map. When doing the phenix.real_space_refine, the CC is slightly increased with respect to the starting structure, the Ramachandran is dramatically increased but some part of the model ( in the case, the first three bases pairs a DNA duplex) are strongly distorted because of a lack of density in the corresponding region of the map. For some reason, this does not append with the MDFF method. I was wondering if there is a mean, in phenix.real_space_refine, to exclude a part of the model from being fitted in the map. Indeed, the distortion I observe in the DNA duplex is likely due to the fact that the real_space_refine tries to put the atoms at the extremity of the duplex in the closest density at the price of a strong distortion of the structure. Thank in advance for your suggestions. 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_3454313285][signature_3433042689][signature_3416814468] -----------------------------------------------

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phenix.combine_focused_maps
by Manoj saxena 10 May '23

10 May '23

Hi , I am trying the following command using PHENIX VERSION: 1.20.1-4487. to generate a composite map from locally refined maps (cryo-EM) of my complex. I have selected multiple regions each one correspond to one of the six locally refined maps that I wish to combine using this command. I would be grateful if you can suggest if this is the correct way to do it. In this test1.pdb contains the complete model. One of my doubts is that if instead of selection, I supply individual model files for each map region can they have multiple chain Ids. Asking because I was told that I would need to combine all chains and rename them as one chain (per map region) to have the correct weighted map. Many thanks Manoj phenix.combine_focused_maps map_file=Relion_deepEmhancer_reference_.mrc map_file=Base_map4.mrc map_file=Base_map1.mrc map_file=Base_map2.mrc map_file=Base_map3.mrc map_file=Base_map5.mrc map_file=Base_map6.mrc model_file=test1.pdb region_selection="(chain P and resid 366-401) or (chain P and resid 179-297) or \ (chain O and resid 401-555) or (chain N and resid 458-530) or (chain N and resid 311-457) or (chain R and resid 13-79) or \ (chain N and resid 726-577) or (chain N and resid 823-880) or (chain I and resid 350-409) or (chain N and resid 577-726) or (chain O and resid 667-722) or \ (chain Q and resid 264-276) or (chain N and resid 928-981) or (chain O and resid 926-971) or \ (chain O and resid 875-899) or (chain Q and resid 208-244) or (chain O and resid 717-739) or (chain N and resid 877-898) or \ (chain M and resid 7-101) or (chain L and resid 2047-2141) or (chain L and resid 1718-1746) or (chain L and resid 2001-2025) or (chain N and resid 880-900) or (chain P and resid 430-440) or (chain L and resid 1954-1965) or (chain P and resid 131-154)" composite_map_file=composite_map.mrc composite_half_map_1_file=composite_half_A_map.mrc composite_half_map_2_file=composite_half_B_map.mrc local_weighting=True rigid_body_refinement_single_unit=False nproc=8 resolution=4.0

2 1

Issue resorting water chain
by Victor Rangel 05 May '23

05 May '23

Dear bb, I'm using phenix.sort_hetatms to sort my water molecule chain based on their bfactor. My macromolecule and water chains are separated, and I'd very much like them to remain so. When adding *preserve_chain_id=True*, the program outputs: *"Warning: no corresponding macromolecule chain match for C 1"*. The program still writes the output pdb, but it changes the water chain name from "C" to "X", and it does not sort them by bfactor. I'm using Phenix 1.20.1-4487 My command is: *phenix.sort_hetatms file_name="refine.pdb" output_file="resorted_refine.pdb" preserve_chain_id=True sort_waters_by=*b_iso* Not sure where my mistake is. Any suggestions? Best, Victor

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Advanced Methods for Ambient Crystallography at ESRF-EBS Workshop - 21-23 November 2023
by Matthew BOWLER 05 May '23

05 May '23

Dear all The ESRF and EMBL Joint Structural Biology Group, with the support of EU project Streamline, is organizing a workshop on sample preparation, data collection and data processing for Ambient Temperature Crystallography. ESRF and EMBL have been laying the groundwork for the future development of this field with two main projects: the refurbishment of MASSIF1 (https://www.esrf.fr/MASSIF1), including a CrystalDirect Harvester, allowing full automation of single crystal RT data collection and the new ID29 (https://www.esrf.fr/id29) for Time Resolved Serial Crystallography experiments with microseconds X-ray pulses. This 2.5 days workshop will cover the different practical and theoretical aspects of room temperature data collection and structure determination on the first day, followed by practicals at the beamlines and data processing on the following days. A total number of 10 participants will be selected and we will accept a limited number of participants’ samples to be tested during the workshop. There is no registration fee and meals and accommodation during the workshop will be provided free of charge. Bursaries are available to cover travel expenses for the participants. Deadline for application for the workshop is on 15th August. Applications can be submitted at the following link https://survey.esrf.fr/index.php/212282?lang=en More information is available at the following link https://www.esrf.fr/home/events/conferences/2023/amax2023.html Confirmed speakers and tutors include: Robert Thorne (Cornell) Marcus Fischer (St Jude) Daniel Keedy (CUNY) Silvia Russi (SSRL) Chia-Ying Huang (PSI) Sasha Popov (ESRF) Clemens Vonhrein (GPhL) Nicolas Coquelle (IBS) -- Matthew Bowler Project Leader MASSIF1@ESRF European Molecular Biology Laboratory 71 avenue des Martyrs CS 90181 F-38042 Grenoble France =================================================== Tel: +33 (0) 4.76.20.76.37 Fax: +33 (0) 4.76.20.71.99 http://www.embl.fr/ http://www.esrf.eu/MASSIF1 https://twitter.com/id30_massif1 https://www.embl.org/people/person/71918b7a010f129de27b37236c7ca90085113d74… ===================================================

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Cryo_fit execution data test GTPases fails
by CUNIASSE Philippe 04 May '23

04 May '23

Dear all, After installing cryo_fit in phenix and gromacs_cryofit on my Macbook Pro M1, I now try to test the code using the example data GTPase. The job encounters immediately a problem but the GUI suggests that the job is still running. The log suggest that the first step did not run successfully (below). I presume setting the topology of the protein but I don’t know. Another question is how is it possible to set other parameters for cryo_fit (like ff…) in the GUI or should I run it in command line ? Thank you for your help and suggestions. Philippe. User's computer's operating system: Darwin ############################################################################################### #################### Step 1: Make gro and topology file by regular gromacs #################### ############################################################################################### Current working directory: /Applications/phenix-1.20.1-4487/modules/cryo_fit/tutorial_input_files/CryoFit_1/steps/1_make_gro command: python 1_before_pdb2gmx_prepare_pdb.py GTPase_activation_center_tutorial.pdb 0 0 0 True Current working directory: /Applications/phenix-1.20.1-4487/modules/cryo_fit/tutorial_input_files/CryoFit_1 This pdb file, /Applications/phenix-1.20.1-4487/modules/cryo_fit/tutorial_input_files/GTPase_activation_center_tutorial.pdb , has 6489 atoms Approximately, for this number of atoms, one 3.1 GHz Intel Core i7 took 7 seconds to make a gro file. command: python 2_runme_make_gro.py /Applications/phenix-1.20.1-4487/modules/cryo_fit/ amber03 True True /usr/local/cryo_fit/cryo_fit/bin// Step 1 didn't run successfully User's command was phenix.cryo_fit /Applications/phenix-1.20.1-4487/modules/cryo_fit/tutorial_input_files/.phenix/project_data/run_1.eff phenix.cryo_fit alone without any arguments introduces full options. If a user sees a message like "Fatal error: Atom xx in residue xx xxx was not found in rtp entry xx with xx atoms while sorting atoms." or "Fatal error: Residue xxx not found in residue topology database" Solution if these residue/atoms are important: Fix wrong names of atoms/residues. Running real_space_refine via phenix GUI will show which atoms need to be fixed. If gromacs amber03 force field doesn't have parameters for these residue/atoms, you may need to add appropriate parameters. If you added parameters, please email me (doonam.kim(a)pnnl.gov), I want to recognize your contribution publicly. Most MD simulation force fields do not support all kinds of rare residue/atoms. cryo_fit2 is under development to address this issue using phenix.eLBOW Solution if these residue/atoms are not important: Remove these "wrong" atoms/residues from user's input pdb file. Run cryo_fit again. Solution if user's input pdb file is big: Probably cryo_fit will change conformation just minimally, I would extract out these "wrong" atoms/residues from user's input pdb file, then add these extracted lines to cryo_fitted file later. Email phenixbb(a)phenix-online.org or doonam.kim(a)pnnl.gov for any feature request/help.

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