- phenixbb - phenix-online.org

convergence in Phenix real space refinement
by Robert Oeffner 20 Oct '23

20 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 15 Oct '23

15 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 10 Oct '23

10 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 05 Oct '23

05 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 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

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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 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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