- phenixbb - phenix-online.org

parallelization of local_grid_search in phenix.real_space_refine?
by Oliver Clarke 10 Feb '18

10 Feb '18

Hi all, phenix.real_space_refine runs pretty decently with run=minimization_global+adp, and the adp part is already parallelized. Using local_grid_search though, it slows down enormously, particularly for large structures, and I’d really like to try using it to correct poorly fit rotamers. Is there any prospect for parallelizing this function? Naively it seems like something that might be amenable to parallelization - so long as adjacent local grids aren’t searched at the same time, it would seem like one might be able to split up the job to run on multiple threads? These days a lot of folks have GPU workstations for cryoEM, which often (in addition to GPUs) have Xeon or Threadripper CPUs with many cores - I’d love to be able to use that computational horsepower effectively for refining my structures. Cheers Oli

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Phenix.molprobity PDB pre-test
by Rune Thomas Kidmose 09 Feb '18

09 Feb '18

Hi, After using Phenix.molprobity I noticed it does a test of the input PDB file in the beginning, where it, among other things, identifies duplicate atom labels and then proceeds to list some of them (and hides the rest some where I guess). It also identifies mismatches between the atom label and the atom type, e.g. if a CB is by mistake listed as an O instead of a C, in the last column in the PDB file. I would like to know if it is possible to somehow call this PDB pre-test function used within phenix.molprobity? or maybe something similar in the phenix package? I would like to use the feature in a small MD pipeline I am developing where the input PDB files are checked for duplicate atoms and mismatches between atom label and type. I believe something like the mentioned pre-test feature would work much better, than my current bash script solutions using combinations of awk, grep, sort, uniq etc. Cheers Ruki

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clashscore
by 潘晓伟 09 Feb '18

09 Feb '18

Hello everyone I refine a cryo EM data with 3.1 angstrom, the model fit well with the map, but the clashscore is high, abot 23. How can I decrease the value of clashscore with realspace.refinement in Phenix GUI. Thanks! Pan ________________________________ xiaowp82(a)hotmail.com

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Computational Crystallography Newsletter, Volume 9, Number 1
by Nigel Moriarty 08 Feb '18

08 Feb '18

I am pleased to announce the publication of the latest issue of the Computational Crystallography Newsletter: http://www.phenix-online.org/newsletter/ A listing of the articles and short communications is given below. Please note that the newsletter accepts articles of a general nature of interest to all crystallographers. Please send any articles to me at NWMoriarty(a)lbl.gov noting that there is a Word Template on the website to streamline production. January 2018 <http://phenix-online.org/newsletter/CCN_2018_01.pdf> Articles - Cβ deviations and other aspects in Amber versus CDL refinements <http://phenix-online.org/newsletter/CCN_2018_01.pdf#page=21> - A few benchmark tests of various compilers on Linux and Windows <http://phenix-online.org/newsletter/CCN_2018_01.pdf#page=25> Short Communications - Tools for model-building with cryo-EM maps <http://phenix-online.org/newsletter/CCN_2018_01.pdf#page=7> - Gemmi – a new MX library <http://phenix-online.org/newsletter/CCN_2018_01.pdf#page=13> - Overfitting to Ramachandran and geometry criteria in the cryoEM Model Challenge <http://phenix-online.org/newsletter/CCN_2018_01.pdf#page=16> Fitting tips #15 – New help to make your 2.5–4Å cryoEM structure even better <http://phenix-online.org/newsletter/CCN_2018_01.pdf#page=2> FAQ - What happens when the Phenix GUI prompts me to send an error report? <http://phenix-online.org/newsletter/CCN_2018_01.pdf#page=6> Cheers Nigel --- Nigel W. Moriarty Building 33R0349, Molecular Biophysics and Integrated Bioimaging Lawrence Berkeley National Laboratory Berkeley, CA 94720-8235 Phone : 510-486-5709 Email : NWMoriarty(a)LBL.gov Fax : 510-486-5909 Web : CCI.LBL.gov

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Residual B values after refinement
by ANAN YUENYAO 07 Feb '18

07 Feb '18

Dear All, I have encountered some error during the PDB validation process after refinement with PHENIX (1.13). After uploading the coordinates and structure factor file, in the header 'Basic coordinate validity', it says that the data contains residual B values. Could anyone please explain the reason behind this error message. Is it going to be problematic for the future PDB deposition? P.S. I have already performed TLS and group B-factor refinement. Thank you in advance! Anan

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FASTA format for sequence file
by egoers＠uoregon.edu 06 Feb '18

06 Feb '18

Hello, I'm trying to run Phase-MR on Phenix (older version) and having trouble formatting my sequence properly. I keep getting error "Protein Sequence not recognized in Composition". I have a good idea of what FASTA should look like (carrot with a name, no spaces or weird characters, followed by the sequence in all capital letter on the next line). I have tried many things, mainly using gedit and plain text files (.txt). I've made sure the file name doesn't have any strange characters as well. If I cut and paste a FASTA file from the PDB into gedit, save that at a .txt, Phaser accepts it. If I cut and paste my protein sequence into the same file, it rejects it. Suggestions?

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how to bypass/deactivate dictionnary check for restraints in phenix.refine
by Maxime Cuypers 02 Feb '18

02 Feb '18

Hello All, I am refining an unusual complex moiety in a protein xl with neutron data. Does anyone know if it is possible to bypass/deactivate dictionnary .cif check i got the blocking error message "it looks like angle and bond restraints are conflicting." and Phenix.refine stops. but really it s not conflicting: my .cif file works great in coot to model the complex. it is hydrogen based, so i really need restraints to get it optimal. any clues welcome, many thanks in advance. Dr. Maxime Cuypers Post-Doctoral Research Associate, Structural Biology St Jude Children s Research Hospital, 262 Danny Thomas Place Memphis, TN 38105-3678, USA

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side-chain on special position.
by Aaron Oakley 02 Feb '18

02 Feb '18

Hello fellow Phenix-ers, I have a structure I am trying to finish in Phenix.refine The is one problem: a glutamate residue sitting on a crystallography 2-fold axis with partial occupancy (picture attached). This residue and its symmetry mate appear to take turns sitting at this position: filling the density leads to severe collision with its symmetry mate. Building the side-chain with occupancy 0.5 doesn’t seem to help, as the residue is pushed out of density during refinement. Any work-arounds? Thanks all, Aaron [cid:[email protected]]

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phenix auto sharpen local sharpening masking artifacts?
by Oliver Clarke 01 Feb '18

01 Feb '18

Hi, I’m trying to run phenix.auto_sharpen with local sharpening, because I have an EM map that has a reasonably substantial variation in local resolution. This is the command I used: phenix.auto_sharpen cryosparc_exp001049_008.mrc resolution=3.26 local_sharpening=true local_aniso_in_local_sharpening=true model.pdb nproc=4 seq_file=seq.fasta >& log & The resulting map looks beautiful (maybe a little too beautiful??) around the model, but shows some funky looking masking artifacts in the density further away from the model (in the micelle region) - see screenshot. Am I doing something wrong? And can I trust that the density is completely free of model bias? Cheers Oli

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Unwanted LINK Records
by Whitley, Matthew J 26 Jan '18

26 Jan '18

Hello all, I am currently refining a structure using Phenix 1.13-2998. Present in this structure is a diphosphate-containing ligand. In the protein chain surrounding the binding site, there is an arginine side chain that points generally toward the diphosphate group, but I cannot define the specific location of the side chain because the side chain density is very poor. The density for the ligand is unambiguous. Upon refinement, Phenix places the Arg side chain so close to the ligand that it draws a covalent bond between the two, and the post-refinement PDB file contains a LINK record for this bond. In reality, the two are not covalently connected, and ideally Phenix would find a conformation for this side chain that is outside of covalent bonding distance. I have tried refining after manually moving the side-chain to a non-clashing position multiple times, but in every case the output PDB contains a LINK for a covalent bond between ligand and side chain. My question: How can I tell Phenix NOT to allow these atoms to come with covalent bonding distance? Is there some kind of "anti-LINK" information I can feed it that will force phenix.refine to select some other conformation for the side chain? Thanks for your advice. Sincerely, Matthew Whitley --- Matthew J. Whitley, Ph.D. Research Instructor Department of Pharmacology & Chemical Biology University of Pittsburgh School of Medicine

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