- phenixbb - phenix-online.org

histo-blood group antigens
by Hansman, Grant (NIH/VRC) [F] 20 Apr '10

20 Apr '10

I want to add a trisaccharide to my structure, but when I run phenix.refine the sugar breaks up. I know I need to specify the links on the sugar and that they must be in the reverse order, but I don't know how to do that. i.e., Some thing like this... which worked fine with a different sugar (below) refinement.pdb_interpretation { apply_cif_link { data_link = ALPHA1-2 residue_selection_1 = chain D and resname GAL and resid 2 residue_selection_2 = chain D and resname FUC and resid 1 } apply_cif_link { data_link = BETA1-3 residue_selection_1 = chain D and resname NGA and resid 3 residue_selection_2 = chain D and resname GAL and resid 2 BUT now I have a new sugar (below is the pdb). I want to create the links, does anyone know how to do this? HETATM 2386 C1 FUC A 1 16.834 10.319 -8.554 1.00 66.42 C HETATM 2387 C2 FUC A 1 16.606 11.012 -7.166 1.00 61.84 C HETATM 2388 C3 FUC A 1 17.009 12.513 -7.241 1.00 59.45 C HETATM 2389 C4 FUC A 1 16.144 13.200 -8.308 1.00 60.73 C HETATM 2390 C5 FUC A 1 16.343 12.478 -9.659 1.00 61.11 C HETATM 2391 C6 FUC A 1 15.451 13.074 -10.752 1.00 58.85 C HETATM 2392 O1 FUC A 1 18.293 10.173 -8.848 1.00 75.63 O HETATM 2393 O2 FUC A 1 17.360 10.357 -6.166 1.00 60.01 O HETATM 2394 O3 FUC A 1 16.815 13.162 -5.990 1.00 59.75 O HETATM 2395 O4 FUC A 1 14.774 13.159 -7.919 1.00 58.98 O HETATM 2396 O5 FUC A 1 16.051 11.063 -9.520 1.00 61.98 O HETATM 2397 C1 GAL A 2 18.717 9.760 -11.037 1.00 85.92 C HETATM 2398 C2 GAL A 2 18.373 9.162 -9.615 1.00 83.98 C HETATM 2399 C3 GAL A 2 19.592 8.289 -9.187 1.00 87.51 C HETATM 2400 C4 GAL A 2 19.814 7.192 -10.269 1.00 87.23 C HETATM 2401 C5 GAL A 2 20.123 7.872 -11.635 1.00 86.28 C HETATM 2402 C6 GAL A 2 20.336 6.876 -12.795 1.00 83.95 C HETATM 2403 O2 GAL A 2 17.629 10.430 -11.635 1.00 91.09 O HETATM 2404 O3 GAL A 2 18.638 6.383 -10.380 1.00 88.24 O HETATM 2405 O4 GAL A 2 19.031 8.744 -12.000 1.00 86.74 O HETATM 2406 O5 GAL A 2 20.641 7.401 -14.059 1.00 79.17 O HETATM 2407 O6 GAL A 2 20.370 8.579 -8.053 1.00 95.12 O HETATM 2408 C1 NGA A 3 20.960 9.184 -6.913 1.00100.54 C HETATM 2409 C2 NGA A 3 20.707 8.446 -5.548 1.00103.23 C HETATM 2410 C3 NGA A 3 20.064 9.437 -4.546 1.00103.55 C HETATM 2411 C4 NGA A 3 21.015 10.661 -4.359 1.00103.72 C HETATM 2412 C5 NGA A 3 21.252 11.342 -5.751 1.00103.24 C HETATM 2413 C6 NGA A 3 22.221 12.560 -5.693 1.00103.28 C HETATM 2414 C7 NGA A 3 20.349 6.053 -6.269 1.00107.39 C HETATM 2415 C8 NGA A 3 19.294 4.961 -6.441 1.00107.38 C HETATM 2416 N2 NGA A 3 19.860 7.256 -5.781 1.00105.47 N HETATM 2417 O3 NGA A 3 19.829 8.805 -3.291 1.00102.40 O HETATM 2418 O4 NGA A 3 22.255 10.230 -3.783 1.00105.38 O HETATM 2419 O5 NGA A 3 21.766 10.375 -6.714 1.00101.87 O HETATM 2420 O6 NGA A 3 22.993 12.697 -6.878 1.00104.86 O HETATM 2421 O7 NGA A 3 21.514 5.860 -6.552 1.00110.32 O END Kindly, Grant

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function to complete sidechains with rotamer
by Joel Bard 19 Apr '10

19 Apr '10

Hi- Is there a way in phenix to fill in missing sidechain atoms with the least clashing rotamer and set those atoms to zero occupancy? Modelers seem to prefer this to completely leaving out the atoms that aren't visible in density. Thanks, Joel

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MTZ files
by Kyle Dolan 18 Apr '10

18 Apr '10

Hi, I am trying to use the Phenix 1.3 software to solve a structure. After using AutoSol to generate initial phases from a MAD experiment at low resolution (5.0 A), I ran AutoBuild using the solve.mtz output file from AutoSol and a .sca file for higher resolution native data that I had collected from a second crystal. Since my target structure includes both protein and DNA, however, I ran several iterations of AutoBuild changing the parameters for building protein or DNA, including different models, playing with rebuild_in_place, etc. But now that I'm ready to move into manual building and refinement, I have a ton of MTZ files from my AutoBuild runs and I don't know which one(s) I should be using for my maps to guide my model-building, and which one I should consider as "the original" to use in a refinement program like phenix.refine or Refmac. Can anyone help put me on the right path? Cheers, Kyle Kyle T. Dolan Department of Biochemistry and Molecular Biology The University of Chicago ktd(a)uchicago.edu

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Fix rotamers
by Jason C Porta 16 Apr '10

16 Apr '10

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structures with problem loops / ligands
by Pavel Afonine 15 Apr '10

15 Apr '10

Hi Everyone, I'm in search of a structure that has poor or nearly no density for some relatively short loops or ligands. My search criteria are (which are flexible): - resolution 2-2.5A (slightly higher, slightly lower is ok); - structure is not large (~5000 atoms is absolute max., less is better so I can run tests quicker); - structure is nearly complete and correct - that is everything is good about the structure (almost ready-to-PDB-deposit) apart from problem loops/ligands; - no data pathologies (twinning, severe incompleteness and the likes); - length of problem loops: from 1 to 10 residues; - no restrictions on data and model use (so the structure id may appear in a future publication as an illustration, of course with all proper credits to the source); - it is desirable but not mandatory that a problem loop has some importance. Please reply to me directly. Thanks in advance! Pavel.

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Gordon Research Conference on Diffraction Methods
by A Leslie 15 Apr '10

15 Apr '10

With apologies for duplicate postings: The biannual Gordon Conference on Diffraction Methods in Structural Biology will be held at Bates College in Lewiston, Maine from 18-23rd July. The program covers all aspects of macromolecular structure solution from crystallization to structure solution and refinement and includes sessions on complementary techniques and the potential of free electron lasers. Many of the leading methods developers will be present and the format of the meeting, with free afternoons, provides ample opportunities for informal discussions. Further details, including a full program and details on the application procedure can be obtained from: http://www.grc.org/programs.aspx?year=2010&program=diffrac We hope to see you there ! Andrew Leslie (Chair) & Ana Gonzalez (Vice Chair) Outline Program: Sunday pm: Macromolecular Structures, Pushing the boundaries Discussion leader: Michael Rossmann 1. ABC Transporters: Doug Rees 2. The Spliceosome : Kyoshi Nagai Monday am: Crystallisation and the diffraction experiment Discussion leader: Zbyszek Dauter 1. Nanolitre crystallisation: Seth Harris 2. Twinning and disorder: Todd Yeates 3. Simulating the diffraction experiment: James Holton 4. Microcrystallography: Gwyndaf Evans Monday pm: Radiation damage and data collection strategies Discussion leader: Vivian Stojanoff 1. Radiation damage, experimental: Elspeth Garman 2. Microbeams: Yanhui Zou 3. Testing data collection strategies with the Pilatus: Marcus Mueller Tues am: Synchrotron developments and automated data processing Discussion leader: Thomas Schneider 1. Synchrotrons, latest developments: Sean Mc Sweeney 2. Synchrotrons, latest developments: Janet Smith 3. Data processing with Xia2/CHEF: Graeme Winter 4. Data processing with AUTOPROC: Clemens Vonrhein Tues pm: Complementary techniques Discussion leader: Ana Gonzales 1. Electron tomography: Sriram Subramaniam 2. SAXS: Hiro Tsuruta 3. Spectroscopy: Carrie Wilmot Weds am: Structure solution and refinement Discussion leader: Paul Adams 1. SAD Phasing: Randy Read 2. Molecular replacement with BALBES: Garib Murshudov 3. PHENIX: Tom Terwilliger 4. TLS: Ethan Merritt Weds pm: Challenging problems/Membrane Proteins Discussion leader: TBC 1. Using cubic lipidic phase: Martin Caffrey 2. Membrane Proteins: Stephen White 3. The Bacterial Ribosome: Venki Ramakrishnan Thurs am: Selected Posters and Map improvement and Model building Discussion leader: Tassos Perrakis 1. COOT: Paul Emsley 2. Modelling nucleic acids: Johan Hattne Thursday pm: Future Methods, FELs, Diffraction imaging Discussion leader: Ed Lattman 1. Anton Barty 2. Serial Crystallography: John Spence and Petra Fromme

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Autobuild with ligand in place?
by Claudia Scotti 15 Apr '10

15 Apr '10

Hallo! Sorry for the probably easy question. I'm trying to rebuild a model with Autobuild. The protein has a ligand, whose density is already well defined, thus that the input for the new autobuild run includes its coordinates as well. When I start the autobuild run, however, I see that the ligand is removed before rebuilding, which leads the program to use the ligand density to try to rebuild loops, thus introducing errors. How can I keep the ligand in place, please? Or is there any alternative solutions? Many thanks, Claudia Claudia Scotti Dipartimento di Medicina Sperimentale Sezione di Patologia Generale Universita' di Pavia Via Ferrata, 1 27100 Pavia Italia Tel. 0039 0382 986335/8/1 Facs 0039 0382 303673 _________________________________________________________________ Hotmail: Free, trusted and rich email service. https://signup.live.com/signup.aspx?id=60969

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completing the description of a residue according to idealized geometry
by Peter Grey 15 Apr '10

15 Apr '10

Dear Phenix users, My crystals contains many copies of cobalt hexamine (used for SAD phasing). Currently the model contains only the cobalt ions (without the amines) and I am looking for a tool that will use the idealized geometry of cobalt hexamine to complete the description of these resdiues, i.e. add ATOM lines for the amines Is there such a tool ? Hoping, Peter

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Phenix.reflection_file_converter enhancement request
by Schubert, Carsten [PRDUS] 15 Apr '10

15 Apr '10

Hi, would it be possible to enhance the reflection file converter so that it can simultaneously write out IOBS and FOBS into the same mtz file? Right now these options seem to be mutually exclusive. The automatic conversion in phenix.refine handles that task automatically, so it should not be too hard to implement. Thanks Carsten

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Re: [phenixbb] Real Space Refinement with marginal data
by Rongjin 15 Apr '10

15 Apr '10

Hi Pavel can you show me how to select some residues that are excluded from refinement? You suggested this earlier but I did not know how to do it. I looked through the manual and I can see how to select a chain, but do not know how to select some residues. Thanks Rongjin ------------------ Original ------------------ From: "Pavel Afonine"<PAfonine(a)lbl.gov>; Date: Thu, Apr 15, 2010 08:08 AM To: "PHENIX user mailing list"<phenixbb(a)phenix-online.org>; Subject: Re: [phenixbb] Real Space Refinement with marginal data Hi Carsten, I was wondering if anyone had experience/advice for real space refinement with phenix using marginal data to 3A. I just did a run (SA, real-space refinement against diff_map, 2 fold NCS, grouped APD, fix_rotamers enabled) were the resulting structure showed lots of disconnected sidechains and some broken main chains. I am just repeating the run w/o real space refinement, may be the combination of SA and real space refinement was a bit harsh, but am wondering what kind of parameters make most sense to tweak in order to avoid having the molecules fall apart. this could be a weight issue (weight between real-space target and restraints). In general I didn't find it too beneficial doing real-space refinement globally, although I've seen cases where it made a good difference (but at higher than 3A resolution). You may try to switch to "simple" target (to make it run much faster) and turn on the weight optimization: real_space_refinement { mode = *simple diff_map target_weights = value *grid_search gradients_ratio rmsd_max_bonds = 0.05 rmsd_max_angles = 5 grid_search_scales = 0.25 0.5 0.75 1 1.25 1.5 1.75 2 2.5 3 } "fix_rotamers=true" (local real-space refinement for the residues that really need it, as determined automatically) is much better option. I thoroughly tested it up to 3A resolution and in all test cases it worked just great. Try it and see what happens for your data. Pavel.

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