- phenixbb - phenix-online.org

bad density for part of the electron density map
by Wei Shi 08 Oct '13

08 Oct '13

Hi all, I am working with a dataset in space P212121, resolution 2.8 amstrong, total completeness of the data 96.2% (98.1%), I/sigma 5.2 (3.1). This is a structure of a transcriptional factor (dimer) with the ligand. Upon ligand binding, there is conformational change in some part of the protein and I used the apo protein structure as a search model, and get a molecular replacement solution. After some rounds of refinement and rebuild (mainly in a region in the C-terminal ligand binding domain), the best refinement I have is as follows. But the electron density map for the C-terminal DNA binding (about 80 residues) is still very bad.... I tried to mutate them to alanine and do refinement and also tried to delete the whole region to do refinement, but both of the strategies didn't give me better density which I could use to rebuild the residues manually. I am wondering whether any of you have any ideas about what might go wrong and any suggestions about what to check or try next. Thank you so much! start final --------------------------------------- R-work: 0.3220 0.3100 R-free: 0.3916 0.3884 RMS(angles): 2.50 1.39 RMS(bonds): 0.016 0.010 Ramachandran outliers: 1.8% (Goal: < 0.2%) Ramachandran favored: 89.0% (Goal: > 98%) Rotamer outliers: 5.4% (Goal: 1%) C-beta outliers: 0 (Goal: 0) Clashscore: 11.50 Overall score: 2.71 Best, Wei

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Re: [phenixbb] metal coordination restrain on alternative conformation
by Zhang yu 07 Oct '13

07 Oct '13

Hi Nigel, Another question. How do I let phenix.refine know that all atoms in my ligand should have the same occupancy for one conformation? The occupancy refinement in phenix.refine assigned different occupancies to atoms in one conformation. Thanks Yu On Tue, Oct 1, 2013 at 6:10 PM, Zhang yu <phenixzyfish(a)gmail.com> wrote: > Thanks > > > On Tue, Oct 1, 2013 at 1:54 PM, Nigel Moriarty <nwmoriarty(a)lbl.gov> wrote: > >> I ran >> >> phenix.metal_coordination >> >> and got the attached. Pass it to phenix.refine. >> >> >> On Mon, Sep 30, 2013 at 6:53 PM, Zhang yu <phenixzyfish(a)gmail.com> wrote: >> >>> Hi Nigel, >>> >>> Thanks. Please see attached PDB file. The structure has two molecules in >>> one ASU. Each of molecule contains 6 protein chains and three Nucleic-acid >>> chains (i.e. chain A, B, C, D, E, F, G, H and I for molecule 1; chain K, L, >>> M, N, O, P, Q, R, and S for molecule 2) >>> >>> There is only one nucleoside-triphosphate and its cognate MG++ in each >>> molecule having alternative conformations (named as conformation A and B). >>> The desired restrains are as follows, >>> >>> In molecule 1, >>> atom_selection_1 = name MG,B and chain N and resname MG and resseq 2004 >>> atom_selection_2 = name OD2 and chain N and resname ASP and resseq 739 >>> distance_ideal = 2.090000 >>> >>> atom_selection_1 = name MG,B and chain N and resname MG and resseq 2004 >>> atom_selection_2 = name O3G, B and chain S and resname CMP and resseq >>> 2001 >>> distance_ideal = 2.090000 >>> >>> atom_selection_1 = name MG,B and chain N and resname MG and resseq 2004 >>> atom_selection_2 = name O1B,B and chain S and resname CMP and resseq >>> 2001 >>> distance_ideal = 2.090000 >>> >>> atom_selection_1 = name MG,A and chain N and resname MG and resseq 2004 >>> atom_selection_2 = name O1B,A and chain S and resname CMP and resseq >>> 2001 >>> distance_ideal = 2.090000 >>> >>> atom_selection_1 = name MG,A and chain N and resname MG and resseq 2004 >>> atom_selection_2 = name O1G,A and chain S and resname CMP and resseq >>> 2001 >>> distance_ideal = 2.090000 >>> >>> In molecule 2, >>> atom_selection_1 = name MG,B and chain D and resname MG and resseq 2004 >>> atom_selection_2 = name OD2 and chain D and resname ASP and resseq 739 >>> distance_ideal = 2.090000 >>> >>> atom_selection_1 = name MG,B and chain D and resname MG and resseq 2004 >>> atom_selection_2 = name O3G, B and chain I and resname CMP and resseq >>> 2001 >>> distance_ideal = 2.090000 >>> >>> atom_selection_1 = name MG,B and chain D and resname MG and resseq 2004 >>> atom_selection_2 = name O1B,B and chain I and resname CMP and resseq >>> 2001 >>> distance_ideal = 2.090000 >>> >>> atom_selection_1 = name MG,A and chain D and resname MG and resseq 2004 >>> atom_selection_2 = name O1B,A and chain I and resname CMP and resseq >>> 2001 >>> distance_ideal = 2.090000 >>> >>> atom_selection_1 = name MG,A and chain D and resname MG and resseq 2004 >>> atom_selection_2 = name O1G,A and chain I and resname CMP and resseq >>> 2001 >>> distance_ideal = 2.090000 >>> >>> >>> >>> >>> >>> On Mon, Sep 30, 2013 at 6:31 PM, Nigel Moriarty <nwmoriarty(a)lbl.gov>wrote: >>> >>>> Can you send the residues involved? >>>> >>>> Nigel >>>> >>>> NB. Any files sent to me will be held in strictest confidence. >>>> >>>> >>>> >>>> On Mon, Sep 30, 2013 at 12:51 PM, Zhang yu <phenixzyfish(a)gmail.com>wrote: >>>> >>>>> Hi everyone, >>>>> >>>>> My structure contains a metal coordinating to some residues, one of >>>>> which has alternative conformations. Phenix doesn't pickup the residue with >>>>> alternative conformation when I tried to generate metal restrains using >>>>> ready.set. >>>>> >>>>> Any idea? Thanks >>>>> >>>>> Yu >>>>> >>>>> _______________________________________________ >>>>> phenixbb mailing list >>>>> phenixbb(a)phenix-online.org >>>>> http://phenix-online.org/mailman/listinfo/phenixbb >>>>> >>>>> >>>> >>>> >>>> -- >>>> Nigel W. Moriarty >>>> Building 64R0246B, Physical Biosciences Division >>>> 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 >>>> >>>> _______________________________________________ >>>> phenixbb mailing list >>>> phenixbb(a)phenix-online.org >>>> http://phenix-online.org/mailman/listinfo/phenixbb >>>> >>>> >>> >> >> >> -- >> Nigel W. Moriarty >> Building 64R0246B, Physical Biosciences Division >> 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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Refinement going wild in latest versions
by Hugues Nury 04 Oct '13

04 Oct '13

Hello everyone, I am experiencing differences with phenix.refine versions 1.8.3 or 1.8.4 compared to 1.8.2. Performing comparable runs, Rs are rising several percents with the latest versions, while marginally decreasing using version 1.8.2. I am a very recent convert to Phenix, so maybe I'm missing something obvious, but here are the details: Refinement strategy is xyz+real space+tls+individual Bs at 3.5 A, using NCS and secondary structure restraints, and weight optimization. Starting R/Rfree are around 24.5/28.5 Part of the problem seems to come from secondary structure restraints, with (many) messages in the log file of the refinement going wild looking like WARNING: could not process nonbonded pair Original error: cctbx Internal Error: /net/clover/scratch1/phenix/phenix-1.8.4-1496/cctbx_project/cctbx/crystal/pair_tables.h(663): CCTBX_ASSERT(j_sym >= 0) failure. pdb=" N GLN B 130 " segid="B " pdb=" O VAL B 115 " segid="B " In log files of refinement with version 1.8.2, there are no such messages, and in either case the definition of beta strands were done automatically by Phenix But even secondary structure restraints are switched off, it starts ok but goes wrong at the beginning of cycle 2, during local real space refinement start: r_work=0.2271 r_free=0.2785 final: r_work=0.2418 r_free=0.2937 And then continue to worsen. Any help appreciated! Cheers, Hugues -- Hugues Nury Institut de Biologie Structurale 41 rue Jules Horowitz, F-38027 Grenoble Cedex 1, France +33 6 52 45 17 79

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REMARK 3 NCS
by Luca Pellegrini 03 Oct '13

03 Oct '13

Hello, I have noticed that Phenix 1.8.4-1496 (as well as 1.8.3-1479) appears to have stopped writing the REMARK 3 NCS in the PDB header. Is this so? It is useful to have that info when it comes to depositing the coordinates. Many thanks, Luca Luca Pellegrini Department of Biochemistry University of Cambridge 80 Tennis Court Road Cambridge CB2 1GA - UK Email: lp212(a)cam.ac.uk Tel: 0044-1223-760469 Fax: 0044-1223-766002 Sanger building, room 3.59

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DEN refinement
by Jan van Agthoven 02 Oct '13

02 Oct '13

Hi everyone, I ran a DEN refinement of my low resolution structure (3.6) to improve my model. I typed in the following command: phenix.den_refine model.pdb data.mtz den.reference_file=reference.pdb reference.params with reference.params saying: refinement.reference_model.reference_group { reference = chain A and resseq 1:953 selection = chain A and resseq 1:953 } refinement.reference_model.reference_group { reference = chain B and resseq 1:687 selection = chain B and resseq 1:687 } because the reference file only contains chain A and chain B. Unfortunately I obtained much worse R factors then with a regular refinement: Start R-work = 0.2798, R-free = 0.3176 Final R-work = 0.3733, R-free = 0.4089 Does someone have an idea what could have go wrong? Thanks,

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phaser error
by Alexander Batyuk 02 Oct '13

02 Oct '13

Dear developers, I'm getting the following error while running phaser: ERROR running main function (UNHANDLED): cctbx Error: Lattice type not specified. It comes when I put one placed model (found in a previous run) and search for another. Phenix version 1.8.4, on OSX 10.8.5 Do you have any suggestions? Best wishes, Alex -- Alex Batyuk The Plueckthun Lab www.bioc.uzh.ch/plueckthun

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MR-SAD in phenix
by LISA 01 Oct '13

01 Oct '13

Hi All, If we have partial model we can run MR_SAD by adding a single new keyword to my AutoSol run: input_partpdb_file=MR.pdb But I only have a mtz file not a pdb file in the molecular replacement result with EM map as the model. How can I combine the EM result with SAD to improve the density? I have Ta6Br12 cluster soaked crystal data. How can I define the cluster? How much of F'' and F' of this cluster at the wavelength of 1.254A? Thank you. Lisa

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Plotting disabled
by Luca Pellegrini 01 Oct '13

01 Oct '13

Hello, Phenix.refine (1.8.4-1496) disables plotting in the GUI, complaining that the libpng15.15.dylib is missing (see screen below). The library is actually there, where Phenix says it should be: /opt/X11/lib/libpng15.15.dylib. How do I get Phenix to load it? I am using Mac OSX 10.6.8. Many thanks, Luca Luca Pellegrini Department of Biochemistry University of Cambridge 80 Tennis Court Road Cambridge CB2 1GA - UK Email: lp212(a)cam.ac.uk Tel: 0044-1223-760469 Fax: 0044-1223-766002 Sanger building, room 3.59

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metal coordination restrain on alternative conformation
by Zhang yu 30 Sep '13

30 Sep '13

Hi everyone, My structure contains a metal coordinating to some residues, one of which has alternative conformations. Phenix doesn't pickup the residue with alternative conformation when I tried to generate metal restrains using ready.set. Any idea? Thanks Yu

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DEN refinement stuck
by Jan van Agthoven 24 Sep '13

24 Sep '13

Hi, I launched a DEN refinement 4 hours ago, and it remain stuck with the following message: ----------coordinate minimization before annealing---------- Running DEN torsion optimization on 1 processors... Running torsion simulated annealing ...trying gamma 0.0, weight 3.0 Is this normal? Is torsion simulated annealing so long? Thanks,

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