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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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