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nucleic acid nomencalture
by riya doreen 30 Apr '10

30 Apr '10

Hi Everyone, I am interested in refining a DNA structure with phenix. However, as soon as I read my PDB, I get a warning for missing restraints: PHENIX could not find geometry restraints in the standard monomer library for one or more residues in the PDB file" what is the correct nomenclature for DNA and RNA for use in PHENIX? Can I access phenix.elbow from the GUI ? Thanks

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NCS problems using phenix GUI on a Mac
by John Pascal 28 Apr '10

28 Apr '10

Hello, I am having difficulties defining NCS parameters using the GUI interface (Mac 10.4.11; phenix 1.6-289). Phenix will automatically select NCS restraint groups and use them during refinement. But if I edit the automated selections to my liking then click on Update and Save, the refinement runs with the original parameters unedited. I have tried reading in a ncs.param file, but it does not get read during the refinement run. Also, an intermittent problem with this GUI is that I am not allowed to "Add" a new restraint group. When I click this button, it just clears out the selections on the last group, and does not add a new group. Any ideas? Thanks. Best, John -- John Pascal, PhD ph 215.503.4596 Assistant Professor fx 215.923.2117 Thomas Jefferson University Biochemistry & Molecular Biology 233 South 10th Street, BLSB 804 Philadelphia, Pennsylvania 19107 ---------------------------------------------------------------- This message was sent using IMP, the Internet Messaging Program.

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How do I make trisaccharide, tetrasaccharides
by Hansman, Grant (NIH/VRC) [F] 28 Apr '10

28 Apr '10

How do I make trisaccharide, tetrasaccharides, etc from single monosaccharides? I.e., how do I join the monosaccharides. Do I use ideal coordinates? Can I join them in coot? I want to make HBGA Trisaccharide B. That is, I want to join FUC-GAL-GLA, it would be FUC (C1)-GAL (O2)-GAL (C2) then GAL (C3)-GAL(O3)-GLA(C1) ATOM 1 C1 FUC A 1 1.410 0.468 -0.410 1.00 10.00 C ATOM 2 C2 FUC A 1 0.120 0.513 -1.233 1.00 10.00 C ATOM 3 C3 FUC A 1 -0.831 -0.576 -0.728 1.00 10.00 C ATOM 4 C4 FUC A 1 -1.016 -0.402 0.783 1.00 10.00 C ATOM 5 C5 FUC A 1 0.359 -0.379 1.454 1.00 10.00 C ATOM 6 C6 FUC A 1 0.185 -0.241 2.967 1.00 10.00 C ATOM 7 O1 FUC A 1 2.007 -0.823 -0.535 1.00 10.00 O ATOM 8 O2 FUC A 1 0.424 0.284 -2.610 1.00 10.00 O ATOM 9 O3 FUC A 1 -2.094 -0.452 -1.385 1.00 10.00 O ATOM 10 O4 FUC A 1 -1.700 0.824 1.044 1.00 10.00 O ATOM 11 O5 FUC A 1 1.116 0.724 0.961 1.00 10.00 O ATOM 1 C1 GAL A 1 1.384 0.161 -0.445 1.00 10.00 C ATOM 2 C2 GAL A 1 0.328 -0.139 -1.512 1.00 10.00 C ATOM 3 C3 GAL A 1 -0.975 0.575 -1.139 1.00 10.00 C ATOM 4 C4 GAL A 1 -1.360 0.176 0.289 1.00 10.00 C ATOM 5 C5 GAL A 1 -0.177 0.454 1.220 1.00 10.00 C ATOM 6 C6 GAL A 1 -0.563 0.093 2.655 1.00 10.00 C ATOM 7 O1 GAL A 1 2.612 -0.476 -0.802 1.00 10.00 O ATOM 8 O2 GAL A 1 0.785 0.328 -2.782 1.00 10.00 O ATOM 9 O3 GAL A 1 -2.011 0.186 -2.044 1.00 10.00 O ATOM 10 O4 GAL A 1 -1.686 -1.213 0.327 1.00 10.00 O ATOM 11 O5 GAL A 1 0.945 -0.328 0.819 1.00 10.00 O ATOM 12 O6 GAL A 1 0.539 0.355 3.526 1.00 10.00 O ATOM 1 C1 GLA A 1 1.424 -0.489 -0.382 1.00 10.00 C ATOM 2 C2 GLA A 1 0.392 -0.498 -1.512 1.00 10.00 C ATOM 3 C3 GLA A 1 -0.650 0.592 -1.244 1.00 10.00 C ATOM 4 C4 GLA A 1 -1.222 0.387 0.163 1.00 10.00 C ATOM 5 C5 GLA A 1 -0.068 0.330 1.166 1.00 10.00 C ATOM 6 C6 GLA A 1 -0.630 0.161 2.579 1.00 10.00 C ATOM 7 O1 GLA A 1 2.043 0.797 -0.316 1.00 10.00 O ATOM 8 O2 GLA A 1 1.044 -0.242 -2.757 1.00 10.00 O ATOM 9 O3 GLA A 1 -1.700 0.498 -2.209 1.00 10.00 O ATOM 10 O4 GLA A 1 -1.958 -0.836 0.206 1.00 10.00 O ATOM 11 O5 GLA A 1 0.783 -0.771 0.859 1.00 10.00 O ATOM 12 O6 GLA A 1 0.446 0.112 3.517 1.00 10.00 O

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AutoBuild error message prime and switch
by Rebecca Oot 28 Apr '10

28 Apr '10

Hi, I'm trying to use the AutoBuild wizard to calculate a prime and switch map. When I hit run I get the following error message: The key ignore_blanks is not in var_type_dict....this means the command-line Wizard needs a conversion in the autobuild.py script under 'Translating inputs' or else in excluded_inputs. Any insight would be appreciated. Thanks Rebecca

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ReadySet for special position metal
by TC Hu 26 Apr '10

26 Apr '10

Dear all, I am refining a structure with a metal ion on a 2-fold axis, coordinated by four histidines, two from the ASU and two from symmetry. I used phenix.ready_set to generate the metal coordination file and input it into phenix.refine. However, phenix.refine complains that the customized angle restraints contain a special position atom and cannot continue. I am using Phenix 1.5.2. Could anyone suggest me how to solve this problem? Thank you! Best, Tiancen

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how to generate sharpened map for input into Pymol
by Daqi Tu 24 Apr '10

24 Apr '10

Hi, I am generating a electron density map figure in pymol for my structure. Since the data is very anisotropic, map sharpening has proven to be quite useful. The structure was solved using Phenix. How do I generate an Xplor style map in Phenix that incorporates sharpening? Thanks. Daqi Tu Postdoc Eck lab Dana-Farber Cancer Institute The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.

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apply_cif_link
by Hansman, Grant (NIH/VRC) [F] 23 Apr '10

23 Apr '10

I am trying to link my sugar molecule (FUC-GAL-NGA-FUC), Lewis y, for phenix.refine, but I keep on getting an error message. I am a beginner at this so I just don't know how to make the links. For , example, I am using this: refinement.pdb_interpretation { apply_cif_link { data_link = BETA1-2 residue_selection_1 = chain C and resname GAL and resid 224 residue_selection_2 = chain C and resname FUC and resid 223 } apply_cif_link { data_link = BETA1-3 residue_selection_1 = chain C and resname GAL and resid 224 residue_selection_2 = chain C and resname NGA and resid 225 } apply_cif_link { data_link = BETA1-3 residue_selection_1 = chain C and resname NGA and resid 225 residue_selection_2 = chain C and resname FUC and resid 226 Number of atoms: 46 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 46 Unusual residues: {'GAL%DEL-HO2%DEL-HO3': 1, 'NGA%DEL-O1%DEL-HO3': 1, 'FUC%DEL-O1': 2} Unexpected atoms: {'NGA%DEL-O1%DEL-HO3,O1L': 1, 'NGA%DEL-O1%DEL-HO3,O': 1} Classifications: {'undetermined': 4} Modifications used: {'DEL-HO2': 1, 'DEL-HO3': 2, 'DEL-O1': 3} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 4 Unresolved non-hydrogen chiralities: 2 Unresolved apply_cif_link angles: 1 Unresolved apply_cif_link chiralities: 1 Number of atoms with unknown nonbonded energy type symbols: 2 "HETATM 5649 O NGA C 225 .*. O " "HETATM 5655 O1L NGA C 225 .*. O " Time building chain proxies: 2.31, per 1000 atoms: 0.41 Sorry: Fatal problems interpreting PDB file: Number of atoms with unknown nonbonded energy type symbols: 2 Please edit the PDB file to resolve the problems and/or supply a CIF file with matching restraint definitions, along with apply_cif_modification and apply_cif_link parameter definitions if necessary (see phenix.refine documentation). Also note that phenix.elbow is available to create restraint definitions for unknown ligands. Any help and direction would be appreciated. Grant

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Conflicting scattering type symbols: refine with TaBr
by Francis E Reyes 23 Apr '10

23 Apr '10

Hi All I'm getting an error refining with TaBr. Got tbr_exp.pdb from Hic-Up and prepared the cif with phenix.elbow. Try to do a refine with the pdb and cif and I get this error. Sorry: Conflicting scattering type symbols: initial symbol: "TA" (from pdb element column) new symbol: "T" (with residue name TBR) atom: "HETATM 1917 TA1 TBR B7131 .*. TA " What are people calling their TaBr records and/or how are they generating their cifs? Thanks F --------------------------------------------- Francis Reyes M.Sc. 215 UCB University of Colorado at Boulder gpg --keyserver pgp.mit.edu --recv-keys 67BA8D5D 8AE2 F2F4 90F7 9640 28BC 686F 78FD 6669 67BA 8D5D

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can phenix.refine create a diff of the current input file with the pdb from the last run before refining?
by Francis E Reyes 22 Apr '10

22 Apr '10

Hi all, Just a feature request that phenix.refine make a diff comparing the current input file with the pdb from the last run and then doing a refinement on the input file and then allow a phenix.refine --revert to allow the user to backtrack incase the refinement isn't suitable. Right now I edit the pdb, save it as xxxx_001-input.pdb and specify xxxx_001-input.pdb as the input file in xxxx_002.def. (Yes I'm using the command line, does the GUI allow this? (i.e. right click on a refinement run then click revert?) ) F --------------------------------------------- Francis Reyes M.Sc. 215 UCB University of Colorado at Boulder gpg --keyserver pgp.mit.edu --recv-keys 67BA8D5D 8AE2 F2F4 90F7 9640 28BC 686F 78FD 6669 67BA 8D5D

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negative density for heavy atom?
by Kelly Daughtry 22 Apr '10

22 Apr '10

Hello all, I have just used phenix autosol and autobuild to phase and build an initial model of my structure with phase information from Tungsten (W), collected at the peak wavelength of 1.2134 Angstroms. Autosol works beautifully! I was able to perform W-SAD and get great maps, when I initially thought I would have to perform W-MAD! The problem I am having is during phenix.refine. When I run the refinement (with and without refining the group anomalous) and including my experimental phases, I see a giant negative peak in the Fo-Fc map at the location of my Tungsten. The rest of the map is beautiful. In the log file, I can tell that the scattering factor is high for tungsten (see below). I believe the negative density is telling me I have too many electrons present at the tungsten site. Can anyone help me figure out what I am doing wrong? I have attached my latest log file. ----------X-ray scattering dictionary---------- Number of scattering types: 7 Type Number sf(0) Gaussians W 1 73.70 2 Se 1 33.92 2 S 11 15.96 2 Mg 1 11.95 2 O 462 7.97 2 N 343 6.97 2 C 1326 5.97 2 sf(0) = scattering factor at diffraction angle 0. ========================== Anomalous scatterer groups ========================= Anomalous scatterer group: Selection: "name W" Number of selected scatterers: 1 f_prime: 16.87 f_double_prime: 17.72 refine: f_double_prime Total number of atoms in anomalous groups: 1 ******************************************************* Kelly Daughtry PhD Candidate Department of Physiology and Biophysics Boston University School of Medicine 590 Commonwealth Ave R 390 Boston MA, 02215 (P) 617-358-5548 *******************************************************

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model vs Wilson b-factor
by Gino Cingolani 22 Apr '10

22 Apr '10

Hi all, we've solved a large structure (~20,000 residues/asymm unit), with 4-fold ncs and diffraction data to 3.3A. The Rfree/Rfac is ~28%-24% with OK geometry with no major outliers in the Ramachandran plot. I would think I'm done (.. after 6 years!). However, my refined model b-factor (~130A2) is >> Wilson b-factor (~80A2). Obviously I'm not too happy with it. Here is what I tried to resolve this discrepancy: --> play with wxu_scale --> play with B-factor weight in ncs restraint (4-fold ncs) --> play with number of macrocycles --> Redefine tls groups So far nothing really works, except switching from individual_adp to group_adp. However, this increases my Rfree by almost 3%. Any ideas? Thanks in advance, Gino ****************************************************************************** Gino Cingolani, Ph.D. Associate Professor Thomas Jefferson University Dept. of Biochemistry & Molecular Biology 233 South 10th Street - Room 826 Philadelphia PA 19107 Office (215) 503 4573 Lab (215) 503 4595 Fax (215) 923 2117 E-mail: gino.cingolani(a)jefferson.edu ****************************************************************************** "Nati non foste per viver come bruti, ma per seguir virtute e canoscenza" ("You were not born to live like brutes, but to follow virtue and knowledge") Dante, The Divine Comedy (Inferno, XXVI, vv. 119-120)

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Phaser question : MR+SAD after refinement
by Peter Grey 22 Apr '10

22 Apr '10

Dear All, I solved a structure by MR+SAD in Phaser, refined it, and would like now to let Phaser locate additional heavy atom. Should I remove the anomalous scatterers from the "PARTIAL PDB" I input to Phaser ? Thank you for your time, Peter

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Error in the end of phenix-refine with NCS
by José Trincão 22 Apr '10

22 Apr '10

Hello, I ran 2 jobs of phenix.refine with ncs (disabled automatic definition) and real-space refinement, weight optimization, 3 macrocycles. In the end of the third macrocycle I got these error messages for both: ===================== NCS restraints at end of refinement ===================== NCS restraint group 1: NCS operator 1: Reference selection: "chain A" Other selection: "chain B" Number of atom pairs: 9281 Traceback (most recent call last): File "/usr/local/phenix-1.6.1-357/phenix/phenix/command_line/refine.py", line 11, in <module> command_line.run(command_name="phenix.refine", args=sys.argv[1:]) File "/usr/local/phenix-1.6.1-357/phenix/phenix/refinement/command_line.py", line 89, in run call_back_handler=call_back_handler) File "/usr/local/phenix-1.6.1-357/phenix/phenix/refinement/driver.py", line 1187, in run out = log) File "/usr/local/phenix-1.6.1-357/cctbx_project/mmtbx/ncs/restraints.py", line 713, in show_operators ncs_operators.show(sites_cart=sites_cart, out=out, prefix=prefix+" ") File "/usr/local/phenix-1.6.1-357/cctbx_project/mmtbx/ncs/restraints.py", line 470, in show prefix=prefix+" ") File "/usr/local/phenix-1.6.1-357/cctbx_project/libtbx/utils.py", line 690, in write file_object.write(str) IOError: [Errno 5] Input/output error What could be the problem? Thanks. Jose José Trincão, PhD CQFB@FCT-UNL 2829-516 Caparica, Portugal "It's very hard to make predictions... especially about the future" - Niels Bohr

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Phenix.refine in WinXP?
by Dima Klenchin 22 Apr '10

22 Apr '10

Now that Phenix has a nice GUI and all that, will there ever be a Windows version? And a similar question: has anyone managed to get phenix.refine from cci_apps for Win32 distribution running? I can't seem to make it run: 1. Installer says run \cci_apps_build\setpaths.bat The script produces an error: ******************************************* Fatal Error: Incomplete libtbx environment\! ******************************************* Please re-run the libtbx/configure.py command. 2. configure.py is found in two places: \cci_apps_sources\libtbx\configure.py \cci_apps_sources\libtbx\command_line\configure.py When I run either of them with command python configure.py I get an error "ImportError: No module named libtbx.env_config" 3. There is no file libtbx.env_config anywhere in the installation. There is file \cci_apps_build\libtbx_env. Placing it in the same directory with configure.py does not help. Even renaming libtbx_env. to libtbx.env_config and running "python configure.py" still gives an error "No module named libtbx.env_config" (?) 4. If I just run phenix.refine executable from its directory, it stops with en error: File "c:\cci_apps_sources\mmtbx\secondary_structure.py", line 941, in run_ksdssp_direct raise RuntimeError, "KSDSSP not available" RuntimeError: KSDSSP not available Thanks in advance for any help! I am comfortable setting any environmental variables manually - just need to know what they should be. Dima

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Phaser and normal mode analysis
by Francois Berenger 21 Apr '10

21 Apr '10

Hello, If I use Phaser's MR_NMA mode, will it introduce clashes into the structure or are they taken care of? Regards, Francois.

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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] 14 Apr '10

14 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 14 Apr '10

14 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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