- phenixbb - phenix-online.org

observed reflections error?
by Joel Tyndall 28 Feb '14

28 Feb '14

Hi all, I have a minor issue with phenix reporting the number of observed reflections in the output pdb file where it appears to be roughly double (120080 ) to what is actually in an mtz file (~65000) from scala. Any suggestions where this number might originate from? Joel _________________________________ Joel Tyndall, PhD Associate Professor in Medicinal Chemistry National School of Pharmacy University of Otago PO Box 56 Dunedin 9054 New Zealand Skype: jtyndall Ph: +64 3 479 7293

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Re: [phenixbb] ERRASER location within rosetta
by Terwilliger, Thomas C 28 Feb '14

28 Feb '14

________________________________ From: Terwilliger, Thomas C Sent: Friday, February 28, 2014 8:42 AM To: Benoît Masquida Cc: Terwilliger, Thomas C Subject: RE: [phenixbb] ERRASER location within rosetta Hi Benoit, I'm sorry for the trouble! The error message, "Sorry, Rosetta version 3.5 or later is needed for ERRASER" is printed if erraser cannot find the file erraser_option.py which should be located in $PHENIX_ROSETTA_PATH/rosetta_tools/ERRASER or $PHENIX_ROSETTA_PATH/tools/ERRASER If you don't have PHENIX_ROSETTA_PATH defined then that would fix it as well. Let me know if this doesn't help! All the best, Tom T ________________________________ From: phenixbb-bounces(a)phenix-online.org [phenixbb-bounces(a)phenix-online.org] on behalf of Benoît Masquida [b.masquida(a)unistra.fr] Sent: Friday, February 28, 2014 8:27 AM To: PHENIX user mailing list Subject: [phenixbb] ERRASER location within rosetta Hello all, I just built rosetta on my Mac OS 10.8.5 and now try to configure ERRASER within the phenix GUI. I correctly indicated the location of the rosetta build and I specified the same location for ERRASER. However when I start an ERRASER job, an error tells me that "ERRASER works with rosetta3.5 or later version". This is strange because i downloaded one of the latest version of rosetta. I don't know if I gave a wrong locate or if my build is corrupted. Any idea from anyone that could have experienced the same problem? pwd outputs this: /Users/benoit1/share/rosetta_2014wk05_bundle/main, where I find database/ and source/ Thanks. Benoit -- Benoît Masquida Chargé de Recherche CNRS GMGM, UMR 7156 GMGM tel: +33 3 68 85 14 81 fax: +33 3 68 85 13 65 IPCB, 21, rue René Descartes 67084 Strasbourg b.masquida(a)unistra.fr<mailto:[email protected]>

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ERRASER location within rosetta
by Benoît Masquida 28 Feb '14

28 Feb '14

Hello all, I just built rosetta on my Mac OS 10.8.5 and now try to configure ERRASER within the phenix GUI. I correctly indicated the location of the rosetta build and I specified the same location for ERRASER. However when I start an ERRASER job, an error tells me that "ERRASER works with rosetta3.5 or later version". This is strange because i downloaded one of the latest version of rosetta. I don't know if I gave a wrong locate or if my build is corrupted. Any idea from anyone that could have experienced the same problem? pwd outputs this: /Users/benoit1/share/rosetta_2014wk05_bundle/main, where I find database/ and source/ Thanks. Benoit -- Benoît Masquida Chargé de Recherche CNRS GMGM, UMR 7156 GMGM tel: +33 3 68 85 14 81 fax: +33 3 68 85 13 65 IPCB, 21, rue René Descartes 67084 Strasbourg b.masquida(a)unistra.fr

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Challenging Refinement at 5 A Resolution
by Erik Walinda 28 Feb '14

28 Feb '14

Dear community, This is my first adventure in crystallography and it seems a rather challenging one. I obtained at dataset at 5.06 A resolution of a 600 residue protein. 3 domains of the protein are already solved by earlier x-ray crystallographic studies. While trying to grow better diffracting crystals and waiting for the next chance to shoot crystals at the synchrotron, I am trying to fit the already solved domains into the electron density of the low data set. Although I tried phaser using the solved structures, I never got a TFZ higher than ~ 6.4. Interestingly, Balbes constructed a model which does not contain any of the already solved domains, but, when using the Balbes output in Phaser, I obtain a TFZ score of 11 and an LLG of 330. (4 molecules / ASU; P2221) If this solution is correct, then in principle it should be possible to fit the already known domains into the structure (I am dreaming of something like a electron-microscopy-type fitting or the early ribosome structures). Phenix refinement however raises the Rfree, instead of lowering it. From my limited knowledge in the field I figured this may be that a) this kind of refinement doesnt work at this resolution or 2) the MR-solution was not really a solution. So I was very excited, when I found the recent papers about DEN refinement and Phenix-Rosetta. I am trying DEN refinement first, using the already solved structures as a reference. The den_refine program nicely creates 2760 DEN restraints. However, after 1 cycle (about 6 h of CPU time at 30 processors), the Rfree goes up (Initial: 0.49; final: 0.57). Indeed, the grid search seems not to be successful, since in the grid search for gamma/w, all Rfree values are rather similar and the lowest Rfree is 0.54. So I would like to ask the community, if ... 1) I shouldn't trust the phaser TFZ score too much and maybe it is just no solution after all? 2) the DEN parameters of phenix.den_refine can be optimized to allow to refine a super-low resolution structure? (I am using the standard parameters from the example: https://www.phenix-online.org/documentation/den_refine.htm) 3) 1 cycle is simply not enough and I should let the computation run for a few days to see, if the Rfree drops down later in the run? 4) Even though Phaser gave me the solution in P2221, may it be that I am trying to refine it in the wrong spacegroup and that's why I fail? Sincerely, Erik

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Re: [phenixbb] unusually high B-factors for selected -heavier- atoms
by Kay Diederichs 27 Feb '14

27 Feb '14

Jan, could it be radiation damage? - that would affect the heavier atoms first/most ... To prove/disprove, use zero-dose extrapolation and re-refine. Kay Am 27.02.14 20:13, schrieb phenixbb-request(a)phenix-online.org: > Date: Thu, 27 Feb 2014 09:50:31 -0800 > From: Jan <jan.abendroth(a)gmail.com> > To: PHENIX user mailing list <phenixbb(a)phenix-online.org> > Subject: [phenixbb] unusually high B-factors for selected -heavier- > atoms > Message-ID: <D87628CC-A657-4B4C-B14F-C230C0C2EF00(a)gmail.com> > Content-Type: text/plain; charset="iso-8859-1" > > Hi all, > I am refining a pretty high resolution structure (1.65?, P1) with two tetramers of the protein in the ASU using Phenix dev 1630. > Refinement statistics looks really good, R=0.16 Rf=0.18, maps are very clear. However, several sulphur atoms of the protein, and in particular the phosphorous atoms of its cofactor NAD have inflated B-factors, along with distinct FoFc peaks. For instance B-factors for a Met with very well defined density: CB=19.7, CG=27.5, SD=62.2, CE=38.4 > > For some of the residues it is comparable when I refine with or without TLS groups. I used one group per chain of this compact protein, the cofactor is part of each TLS group. Restraints for NAD were generated via eLBOW. When I refine the structure in refmac, using either the standard cif file or the eLBOW generated one, B-factors remain low. > > Any ideas? I am happy to share the data. It is a SSGCID target and will be in the PDB shortly anyway. > > Thanks, > Jan > > > > -- > Jan Abendroth > Emerald BioStructures > Seattle / Bainbridge Island WA, USA > home: Jan.Abendroth_at_gmail.com > work: JAbendroth_at_embios.com > http://www.emeraldbiostructures.com >

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unusually high B-factors for selected -heavier- atoms
by Jan 27 Feb '14

27 Feb '14

Hi all, I am refining a pretty high resolution structure (1.65Å, P1) with two tetramers of the protein in the ASU using Phenix dev 1630. Refinement statistics looks really good, R=0.16 Rf=0.18, maps are very clear. However, several sulphur atoms of the protein, and in particular the phosphorous atoms of its cofactor NAD have inflated B-factors, along with distinct FoFc peaks. For instance B-factors for a Met with very well defined density: CB=19.7, CG=27.5, SD=62.2, CE=38.4 For some of the residues it is comparable when I refine with or without TLS groups. I used one group per chain of this compact protein, the cofactor is part of each TLS group. Restraints for NAD were generated via eLBOW. When I refine the structure in refmac, using either the standard cif file or the eLBOW generated one, B-factors remain low. Any ideas? I am happy to share the data. It is a SSGCID target and will be in the PDB shortly anyway. Thanks, Jan -- Jan Abendroth Emerald BioStructures Seattle / Bainbridge Island WA, USA home: Jan.Abendroth_at_gmail.com work: JAbendroth_at_embios.com http://www.emeraldbiostructures.com

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FAQ high res refinement
by Eike Schulz 27 Feb '14

27 Feb '14

> > Dear all, > > I am currently refining a rather well resolved protein at 0.97Å. However, even > after many cycles of refinement the R-factors are stuck at around Rwork/Rfree > 14.5/16.5. Considering number of aa, Rmerge (3.5%) and resolution this seems > to be too high. I assume 10 25 macrocycles should be enough for effective > weight refinement in phenix, however no improvement of the R-factors. > > A quick run with default settings in competitor software 'R' yields >2% better > R-factors. > > I would appreciate suggestion how to improve my refinement protocol, values > differing from default are listed below. > > Thank you very much in advance > > Eike > > > > > > > refine { > adp { > individual { > isotropic = element H > anisotropic = not element H > } > group_adp_refinement_mode = one_adp_group_per_residue \ > *two_adp_groups_per_residue group_selection > } > } > main { > apply_overall_isotropic_scale_to_adp = False > nqh_flips = False > ordered_solvent = True > place_ions = True > number_of_macro_cycles = 10 > hydrogen_bonds = True > use_convergence_test = True > target = auto *ml mlhl ml_sad ls > random_seed = 3326496 > wavelength = 0.885611 > nproc = 4 > } > hydrogens { > refine = individual *riding Auto > } > tls { > find_automatically = False > one_residue_one_group = False > } > ordered_solvent { > mode = second_half filter_only every_macro_cycle \ > *every_macro_cycle_after_first > h_bond_min_mac = 1 > h_bond_min_sol = 1 > h_bond_max = 6 > refine_occupancies = True > new_solvent = isotropic *anisotropic > b_iso_min = 0 > } > peak_search { > max_number_of_peaks = 1303 > } > target_weights { > optimize_xyz_weight = True > optimize_adp_weight = True > wxc_scale = 0.2 > wxu_scale = 0.2

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Option for renumber the pdb
by Rojan Shrestha 27 Feb '14

27 Feb '14

Hello, I have found the program phenix.pdbtools. Maybe, it can renumber residues of pdb. I have found the options renumber_residues options but I am unable to see the options for starting residues. I have pdb starts from 1 and want to renumber 1 into 250. Can somebody tell me how to put the option for starting residue? Regards, Rojan

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scaling in phenix.fobs_minus_fobs_map
by Michael Thompson 27 Feb '14

27 Feb '14

Hello, I have a very simple question about phenix.fobs_minus_fobs_map, and it's implementation in the GUI. I just want to make sure I am not skipping an important step in generating my isomorphous difference map. I'm trying to create an Fo-Fo map for two data sets at pretty different resolutions, using phases from a model. I truncated the higher-res data so the high resolution limit matches the lower-res data set. Are these 2 mtz files sufficient for input into phenix.fobs_minus_fobs_map, or do I need to use another utility to scale the two data sets together prior to calculating the map coefficients? I suppose another way to ask my question would be, does phenix.fobs_minus_fobs_map perform scaling of the two Fobs arrays before calculating the new map? Thanks for clarifying, Mike -- Michael C. Thompson Graduate Student Biochemistry & Molecular Biology Division Department of Chemistry & Biochemistry University of California, Los Angeles miket(a)chem.ucla.edu

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problem phenix ensemble
by Firas FADEL 25 Feb '14

25 Feb '14

Hello, I am using phenix ensemble to refine an X-ray structure of a protein (40kDa) at 1.05 A in complex with a ligand. The occupancy of the ligand is 73%. After refining the structure, I found out that the program confused the position of the ligand and put some water molecules. Do you have any suggestion or a command to avoid this problem. If you need details I can send you the mtz and pdb files. Thanks in advance. Firas Fadel Firas FADEL Institut de Génétique et de Biologie Moléculaire et Cellulaire, IGBMC Equipe Alberto PODJARNY, 1 Rue Laurent Fries, 67404 Illkirch-France Email : fadel(a)igbmc.fr<mailto:[email protected]> Tel: + 33 (0) 3 88 65 33 13<tel:%2B%2033%20%280%29%203%2088%2065%2033%2013>

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