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autobuild 'hires_file'
by Bryan W. Lepore 07 Nov '07

07 Nov '07

i have phenix 2007_08_18_1856, (and i think latest cci apps). i have a jumble of questions, i'll try step by step: [1 A] in phenix.autobuild, e.g. a SAD dataset, does the flag 'hires_file=w1.sca' (help says "Merge in hires data"), mean that phases will be extended to a high resolution limit as found in w1.sca? (vide infra) [1 B] can the labels be the same as the 'other' data (the documentation suggests this)? i have tried a few things like : phenix.autobuild data=resolve.mtz hires_file=high_resolution.mtz input_hires_labels='FPnat SIGFPnat' seq_file=seq.txt ... and i see Cell: [99.810997009277344, 99.810997009277344, 140.37300109863281, 90.0, 90.0, 90.0] New resolution: 2.20520367253 High-res file input labels: ['FPnat', 'SIGFPnat'] ... which is good, but the job promptly fails with this cryptic (to me) error message: ************************************************************ Failed to carry out AutoBuild_datafile_info_inputs: 'all_input_hires_labels' ************************************************************ ... (google:all_input_hires_labels and looking through docs quick didn't find it) -bryan

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PDB deposition of tls refined structure
by Rene Jorgensen 01 Nov '07

01 Nov '07

Dear phenix users, I am about to deposit a 2.5A structure at the PDB. The structure has been refined using phenix.refine with strategy=tls+individual_sites +individual_adp, which actually works very well but (because of the tls refinement) also results in the output of ANISOU records for the atoms in the PDB file. When using PDB_extract during the PDB submission process the ANISOU record is picked up as regular anisotropic refinement although the resolution is too low for that. Should I just accept it and leave it as it is or should I correct the info in the Auto Dep Input Tool (ADIT) to isotropic with just the regular b-factor values? Thanks in advance, Rene Jorgensen

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Pango
by Frank von Delft 01 Nov '07

01 Nov '07

Hi, I just installed the latest phenix version (long overdue), and it burps with the following when I try to run the GUI. Looks like an absolute path was left lying around, no? Cheers phx ---------------------------------------------------- Running the PHENIX GUI with /usr/local/phenix/1.3b/phenix-1.3b/build/intel-linux-2.4/base/bin/python PHENIX distribution located in /usr/local/phenix/1.3b/phenix-1.3b/phenix Shell variable SSH_PATH not set Variable PYMOL_PATH set to /usr/local/phenix/1.3b/phenix-1.3b/pymol Shell variable RSH_PATH not set (python:31886): Pango-WARNING **: No builtin or dynamically loaded modules were found. Pango will not work correctly. This probably means there was an error in the creation of: '/net/ribbon/scratch1/phenix/phenix-1.3b/build/intel-linux-2.4/base/etc/pango/pango.modules' You should create this file by running pango-querymodules. (python:31886): Pango-WARNING **: pango_shape called with bad font, expect ugly output (python:31886): Pango-WARNING **: pango_font_get_glyph_extents called with null font argument, expect ugly output (python:31886): Pango-WARNING **: pango_font_get_metrics called with null font argument, expect ugly output (python:31886): Pango-WARNING **: _pango_cairo_font_install called with bad font, expect ugly output ----------------------------------------------------

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Re: [phenixbb] lower limits on grid spacing/binning
by Ralf W. Grosse-Kunstleve 31 Oct '07

31 Oct '07

Probably, the original poster already got more than he bargained for, but for the records, a few more comments: > All FFT based structure factor programs require that the sampling > rates along each axis be even. I don't think this is true, unless I'm misunderstanding what "sampling rate" means. The FFT in phenix is based on FFTPACK (written in the 80s) which works for any number of grid points. FFTw also supports arbitrary gridding. > They may have other required factors > depending on the space group, but they will be happy to inform you > if you make a choice it doesn't like. They are also more efficient > when the prime factors of the sampling rates are small numbers. Try > to stick with multiples of 2,3, and 5 if possible. That's good advice. FFTPACK is fastest for transform sizes that are multiples of 2,3,4 and 5. The map calculation algorithms in phenix automatically take this into account. > All FFT programs will fail if you > sample your map courser than twice that frequency, as SFALL did for > you. This may be true for SFALL, but not for the FFT algorithms in the phenix libraries ($PHENIX/cctbx/include/cctbx/maptbx/structure_factors.h). The critical reference is: David A. Langs (2002), J. Appl. Cryst. 35, 505. As short as it is, this was an incredibly important paper. In retrospect, it is amazing that it took so long for someone to discover the trick. Ralf

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lower limits on grid spacing/binning
by Terry Lang 30 Oct '07

30 Oct '07

Hey Everyone, I have been told by several crystallographers that the general rule of thumb for grid spacing when generating a map is one third the resolution (eg If your crystal structure has a resolution of 1.2 A, your grid spacing should be 0.4). Is there a mathematical reason why this ratio should be maintained or is this simply a holdover from slower computers with lower memory? More importantly for my application, is there a lower limit on how fine the grid spacing can be? In other words, is there a lower limit at which one is oversampling the data for a particular resolution? Any information and/or references would be greatly appreciated. Sincerely, Terry -- P. Therese Lang Post Doc Alber Lab, UC Berkeley

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linking residues question
by Crystal K. Chuang 26 Oct '07

26 Oct '07

Hello all, I was wondering if there is a tool in RESOLVE that, when used through PHENIX, links up individual chains of residues and ties in symmetry related fragments so that, as a result, packs everything together to generate more of a globular unit? Many thanks, -Crystal

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NCS interpretation
by Claudia Scotti 25 Oct '07

25 Oct '07

Dear list, I'm trying to undestand the NCS symmetry in a unit cell with 8 molecules (2 A resolution). The unit cell is almost orthorhombic (68.900 79.240 90.040 89.97 90.04 89.97), but only P1 + twinning worked for MR and for refining the structure (Rfree=0.22; Rcryst=0.18). The crystal simulated a P222 space group (the best seemed to be P21212), so I'd expect NCS axis parallel to . Now I've used phenix.simple_ncs_from_pdb to get the symmtery operators (see ouput below). I've read the manual, but I'm nevertheless finding it difficult to " see" the NCS axis. Any suggestions, please, on how to interpret the output, please, and "draw" the axis or on any alternatives on how to proceed? Many many thanks and a huge apology for the naive question (this is only my third strutcure...). Claudia --------------------------------------------------------------------------- # simple_ncs_from_pdb # # Find ncs among chains in a PDB file # type simple_ncs_from_pdb --help for help Parameters used for simple_ncs_from_pdb: find_ncs { temp_dir = "" min_length = 10 njump = 1 njump_recursion = 10 min_length_recursion = 50 min_percent = 95 max_rmsd = 2 quick = True max_rmsd_user = 3 domain_finding_parameters { find_invariant_domains = True initial_rms = 0.5 match_radius = 2 similarity_threshold = 0.75 smooth_length = 0 min_contig_length = 3 min_fraction_domain = 0.2 max_rmsd_domain = 2 } verbose = False } Chains in this PDB file: ['A', 'B', 'C', 'D', 'E', 'F', 'G', 'H'] GROUPS BASED ON QUICK COMPARISON: [['A', 'B', 'C', 'D', 'E', 'F', 'G', 'H']] Looking for invariant domains for ...: ['A', 'B', 'C', 'D', 'E', 'F', 'G', 'H'] [[[19, 130], [148, 253]], [[21, 130], [148, 253]], [[21, 130], [148, 253]], [[19, 128], [149, 253]], [[19, 130], [148, 253]], [[21, 128], [148, 253]], [[19, 130], [149, 253]], [[21, 129], [149, 253]]] GROUP 1 Summary of NCS group with 8 operators: ID of chain/residue where these apply: [['A', 'B', 'C', 'D', 'E', 'F', 'G', 'H'], [[[20, 117], [121, 130], [149, 253]], [[20, 117], [121, 130], [149, 253]], [[20, 117], [121, 130], [149, 253]], [[20, 117], [121, 130], [149, 253]], [[20, 117], [121, 130], [149, 253]], [[20, 117], [121, 130], [149, 253]], [[20, 117], [121, 130], [149, 253]], [[20, 117], [121, 130], [149, 253]]]] RMSD (A) from chain A: 0.0 0.46 0.47 0.53 0.54 0.48 0.48 0.59 Number of residues matching chain A:[213, 212, 212, 211, 212, 210, 213, 211] Source of NCS info: sortwaterxyzout.pdb OPERATOR 1 CENTER: 19.3475 -10.7352 7.9738 ROTA 1: 1.0000 0.0000 0.0000 ROTA 2: 0.0000 1.0000 0.0000 ROTA 3: 0.0000 0.0000 1.0000 TRANS: 0.0000 0.0000 0.0000 OPERATOR 2 CENTER: 53.8092 24.2127 11.0612 ROTA 1: 0.9998 0.0043 -0.0190 ROTA 2: 0.0045 -0.9999 0.0114 ROTA 3: -0.0190 -0.0115 -0.9998 TRANS: -34.3014 13.1765 20.2795 OPERATOR 3 CENTER: 55.6227 -15.2644 6.2461 ROTA 1: -0.9928 -0.0019 -0.1198 ROTA 2: -0.0045 -0.9986 0.0530 ROTA 3: -0.1197 0.0532 0.9914 TRANS: 75.3327 -25.9880 9.2016 OPERATOR 4 CENTER: 21.4489 28.7297 12.8232 ROTA 1: -0.9923 0.0066 0.1235 ROTA 2: -0.0001 0.9985 -0.0545 ROTA 3: -0.1236 -0.0541 -0.9909 TRANS: 38.7377 -38.6213 24.9897 OPERATOR 5 CENTER: 33.2332 16.3336 52.0552 ROTA 1: 0.9959 0.0207 -0.0884 ROTA 2: -0.0168 0.9988 0.0450 ROTA 3: 0.0892 -0.0433 0.9951 TRANS: -9.4176 -28.8046 -46.0499 OPERATOR 6 CENTER: 35.8216 -23.2140 56.1297 ROTA 1: -0.9985 -0.0249 -0.0490 ROTA 2: -0.0273 0.9985 0.0479 ROTA 3: 0.0477 0.0492 -0.9976 TRANS: 57.2101 10.9031 63.4545 OPERATOR 7 CENTER: 70.2188 11.8599 54.2973 ROTA 1: -0.9987 0.0207 0.0473 ROTA 2: -0.0234 -0.9981 -0.0569 ROTA 3: 0.0460 -0.0580 0.9973 TRANS: 86.6599 5.8364 -48.7180 OPERATOR 8 CENTER: 67.5293 -27.9008 58.5120 ROTA 1: 0.9959 -0.0146 0.0888 ROTA 2: -0.0120 -0.9995 -0.0303 ROTA 3: 0.0892 0.0291 -0.9956 TRANS: -53.5269 -35.9247 61.0251 NCS operators written in format for resolve to: simple_ncs_from_pdb.resolve NCS operators written in format for phenix.refine to: simple_ncs_from_pdb.ncs NCS written as ncs object information to: simple_ncs_from_pdb.ncs_spec Claudia Scotti Dipartimento di Medicina Sperimentale Sezione di Patologia Generale Universita' di Pavia Piazza Botta, 10 27100 Pavia Italia Tel. 0039 0382 986335/8/1 Facs 0039 0382 303673 _________________________________________________________________ Explore the seven wonders of the world http://search.msn.com/results.aspx?q=7+wonders+world&mkt=en-US&form=QBRE

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Re: [phenixbb] NCS interpretation
by Thomas C. Terwilliger 25 Oct '07

25 Oct '07

Hi Claudia, It looks to me like your ncs is almost exactly 222 symmetry, plus a centering. You can tell it is 222 symmetry because all the operators are zeroes except along the diagonal, and the diagonal elements are all 1 or -1 (or close to it). That means that the 4 unique operators go like: x y z -x -y z -x y -z x -y -z The 8 operators appear to be 2 sets of 4, with a centering operation... I made a little PDB file (at the end of this message) that shows the symmetry in these operators. If you run phenix.simple_ncs_from_pdb on it you should get back something similar to your operators. If you run the phenix.autobuild wizard one cycle of rebuilding (not rebuild_in_place) then it will try to find the most compact arrangement of your molecules, and it will also try to find the point group(s) of the molecule... in this case I think it will fail to find the point group though (as it failed with my test model made from your operators). Question: do your molecules pack nicely with this arrangement? -Tom T CRYST1 68.900 79.240 90.040 89.97 90.04 89.97 P 1 1 ORIGX1 1.000000 0.000000 0.000000 0.00000 ORIGX2 0.000000 1.000000 0.000000 0.00000 ORIGX3 0.000000 0.000000 1.000000 0.00000 SCALE1 0.014514 -0.000008 0.000010 0.00000 SCALE2 0.000000 0.012620 -0.000007 0.00000 SCALE3 0.000000 0.000000 0.011106 0.00000 ATOM 1 N GLY A 11 14.343 3.315 16.927 1.00 45.51 ATOM 2 CA GLY A 11 14.811 1.998 17.345 1.00 45.51 ATOM 3 C GLY A 11 15.247 1.270 16.077 1.00 45.51 ATOM 4 O GLY A 11 14.898 1.674 14.948 1.00 45.51 ATOM 5 N GLY A 12 16.012 0.197 16.221 1.00 45.51 ATOM 6 CA GLY A 12 16.552 -0.502 15.059 1.00 45.51 ATOM 7 C GLY A 12 16.175 -1.959 15.092 1.00 45.51 ATOM 8 O GLY A 12 16.336 -2.626 16.122 1.00 45.51 ATOM 9 N GLY A 13 15.633 -2.483 13.985 1.00 45.51 ATOM 10 CA GLY A 13 15.426 -3.925 13.898 1.00 45.51 ATOM 11 C GLY A 13 16.417 -4.451 12.863 1.00 45.51 ATOM 12 O GLY A 13 16.869 -3.746 11.948 1.00 45.51 ATOM 13 N GLY A 14 16.817 -5.708 13.039 1.00 45.51 ATOM 14 CA GLY A 14 17.838 -6.300 12.198 1.00 45.51 ATOM 15 C GLY A 14 17.499 -7.728 11.801 1.00 45.51 ATOM 16 O GLY A 14 16.579 -8.347 12.326 1.00 45.51 ATOM 17 N GLY A 15 18.236 -8.243 10.821 1.00 45.51 ATOM 18 CA GLY A 15 18.016 -9.590 10.322 1.00 45.51 ATOM 19 C GLY A 15 18.896 -9.857 9.116 1.00 45.51 ATOM 20 O GLY A 15 19.799 -9.094 8.774 1.00 45.51 ATOM 21 N GLY A 16 18.579 -10.960 8.439 1.00 45.51 ATOM 22 CA GLY A 16 19.312 -11.427 7.265 1.00 45.51 ATOM 23 C GLY A 16 18.358 -11.735 6.103 1.00 45.51 ATOM 24 O GLY A 16 17.381 -12.470 6.253 1.00 45.51 ATOM 25 N GLY A 17 18.665 -11.180 4.919 1.00 45.51 ATOM 26 CA GLY A 17 17.900 -11.402 3.696 1.00 45.51 ATOM 27 C GLY A 17 17.912 -12.860 3.238 1.00 45.51 ATOM 28 O GLY A 17 18.722 -13.663 3.702 1.00 45.51 ATOM 29 N GLY A 18 17.039 -13.175 2.273 1.00 45.51 ATOM 30 CA GLY A 18 16.903 -14.515 1.711 1.00 45.51 ATOM 31 C GLY A 18 18.197 -15.177 1.241 1.00 45.51 ATOM 32 O GLY A 18 18.412 -16.379 1.421 1.00 45.51 ATOM 33 N GLY A 19 19.088 -14.380 0.652 1.00 45.51 ATOM 34 CA GLY A 19 20.343 -14.917 0.178 1.00 45.51 ATOM 35 C GLY A 19 21.578 -14.472 0.955 1.00 45.51 ATOM 36 O GLY A 19 22.675 -14.340 0.406 1.00 45.51 ATOM 37 N GLY A 20 21.386 -14.238 2.266 1.00 45.51 ATOM 38 CA GLY A 20 22.494 -14.027 3.191 1.00 45.51 ATOM 39 C GLY A 20 22.894 -12.620 3.608 1.00 45.51 ATOM 40 O GLY A 20 23.593 -12.505 4.614 1.00 45.51 ATOM 41 N GLY A 21 22.517 -11.538 2.925 1.00 45.51 ATOM 42 CA GLY A 21 22.940 -10.189 3.303 1.00 45.51 ATOM 43 C GLY A 21 22.343 -9.681 4.631 1.00 45.51 ATOM 44 O GLY A 21 21.143 -9.824 4.862 1.00 45.51 ATOM 45 N GLY A 22 23.105 -9.075 5.551 1.00 45.51 ATOM 46 CA GLY A 22 22.566 -8.357 6.707 1.00 45.51 ATOM 47 C GLY A 22 21.798 -7.088 6.339 1.00 45.51 ATOM 48 O GLY A 22 22.103 -6.402 5.353 1.00 45.51 ATOM 49 N GLY A 23 20.753 -6.790 7.130 1.00 45.51 ATOM 50 CA GLY A 23 20.048 -5.519 6.978 1.00 45.51 ATOM 51 C GLY A 23 19.765 -4.940 8.347 1.00 45.51 ATOM 52 O GLY A 23 19.689 -5.665 9.347 1.00 45.51 ATOM 53 N GLY A 24 19.555 -3.628 8.334 1.00 45.51 ATOM 54 CA GLY A 24 19.129 -2.901 9.522 1.00 45.51 ATOM 55 C GLY A 24 18.093 -1.892 9.118 1.00 45.51 ATOM 56 O GLY A 24 18.258 -1.184 8.123 1.00 45.51 ATOM 57 N GLY A 25 17.006 -1.822 9.877 1.00 45.51 ATOM 58 CA GLY A 25 15.964 -0.840 9.590 1.00 45.51 ATOM 59 C GLY A 25 15.738 0.058 10.803 1.00 45.51 ATOM 60 O GLY A 25 15.499 -0.461 11.884 1.00 45.51 ATOM 61 N GLY A 26 15.823 1.380 10.651 1.00 45.51 ATOM 62 CA GLY A 26 15.526 2.319 11.738 1.00 45.51 ATOM 63 C GLY A 26 14.091 2.813 11.699 1.00 45.51 ATOM 64 O GLY A 26 13.604 3.245 10.648 1.00 45.51 ATOM 65 N GLY A 27 13.366 2.776 12.830 1.00 45.51 ATOM 66 CA GLY A 27 11.964 3.126 12.862 1.00 45.51 ATOM 67 C GLY A 27 11.719 4.242 13.876 1.00 45.51 ATOM 68 O GLY A 27 12.295 4.231 14.981 1.00 45.51 ATOM 69 N GLY B 31 48.655 10.108 2.312 1.00 45.51 ATOM 70 CA GLY B 31 49.109 11.422 1.870 1.00 45.51 ATOM 71 C GLY B 31 49.565 12.166 3.121 1.00 45.51 ATOM 72 O GLY B 31 49.240 11.774 4.261 1.00 45.51 ATOM 73 N GLY B 32 50.323 13.241 2.951 1.00 45.51 ATOM 74 CA GLY B 32 50.881 13.956 4.094 1.00 45.51 ATOM 75 C GLY B 32 50.497 15.410 4.052 1.00 45.51 ATOM 76 O GLY B 32 50.636 16.066 3.011 1.00 45.51 ATOM 77 N GLY B 33 49.974 15.945 5.163 1.00 45.51 ATOM 78 CA GLY B 33 49.762 17.387 5.237 1.00 45.51 ATOM 79 C GLY B 33 50.770 17.929 6.247 1.00 45.51 ATOM 80 O GLY B 33 51.243 17.236 7.161 1.00 45.51 ATOM 81 N GLY B 34 51.161 19.186 6.049 1.00 45.51 ATOM 82 CA GLY B 34 52.195 19.792 6.864 1.00 45.51 ATOM 83 C GLY B 34 51.857 21.223 7.251 1.00 45.51 ATOM 84 O GLY B 34 50.925 21.832 6.736 1.00 45.51 ATOM 85 N GLY B 35 52.610 21.752 8.210 1.00 45.51 ATOM 86 CA GLY B 35 52.394 23.104 8.698 1.00 45.51 ATOM 87 C GLY B 35 53.295 23.388 9.884 1.00 45.51 ATOM 88 O GLY B 35 54.208 22.633 10.217 1.00 45.51 ATOM 89 N GLY B 36 52.986 24.498 10.554 1.00 45.51 ATOM 90 CA GLY B 36 53.739 24.981 11.709 1.00 45.51 ATOM 91 C GLY B 36 52.806 25.299 12.885 1.00 45.51 ATOM 92 O GLY B 36 51.823 26.028 12.745 1.00 45.51 ATOM 93 N GLY B 37 53.138 24.758 14.069 1.00 45.51 ATOM 94 CA GLY B 37 52.395 24.991 15.304 1.00 45.51 ATOM 95 C GLY B 37 52.409 26.454 15.745 1.00 45.51 ATOM 96 O GLY B 37 53.207 27.256 15.256 1.00 45.51 ATOM 97 N GLY B 38 51.553 26.777 16.722 1.00 45.51 ATOM 98 CA GLY B 38 51.422 28.123 17.272 1.00 45.51 ATOM 99 C GLY B 38 52.722 28.796 17.709 1.00 45.51 ATOM 100 O GLY B 38 52.928 29.996 17.511 1.00 45.51 ATOM 101 N GLY B 39 53.627 28.009 18.290 1.00 45.51 ATOM 102 CA GLY B 39 54.889 28.557 18.734 1.00 45.51 ATOM 103 C GLY B 39 56.111 28.108 17.939 1.00 45.51 ATOM 104 O GLY B 39 57.218 27.987 18.468 1.00 45.51 ATOM 105 N GLY B 40 55.895 27.858 16.634 1.00 45.51 ATOM 106 CA GLY B 40 56.986 27.642 15.691 1.00 45.51 ATOM 107 C GLY B 40 57.384 26.232 15.283 1.00 45.51 ATOM 108 O GLY B 40 58.065 26.108 14.265 1.00 45.51 ATOM 109 N GLY B 41 57.025 25.156 15.985 1.00 45.51 ATOM 110 CA GLY B 41 57.447 23.804 15.614 1.00 45.51 ATOM 111 C GLY B 41 56.827 23.279 14.304 1.00 45.51 ATOM 112 O GLY B 41 55.623 23.414 14.094 1.00 45.51 ATOM 113 N GLY B 42 57.575 22.665 13.377 1.00 45.51 ATOM 114 CA GLY B 42 57.017 21.932 12.239 1.00 45.51 ATOM 115 C GLY B 42 56.262 20.664 12.636 1.00 45.51 ATOM 116 O GLY B 42 56.589 19.990 13.624 1.00 45.51 ATOM 117 N GLY B 43 55.203 20.352 11.869 1.00 45.51 ATOM 118 CA GLY B 43 54.507 19.080 12.049 1.00 45.51 ATOM 119 C GLY B 43 54.201 18.484 10.692 1.00 45.51 ATOM 120 O GLY B 43 54.103 19.197 9.686 1.00 45.51 ATOM 121 N GLY B 44 53.997 17.171 10.724 1.00 45.51 ATOM 122 CA GLY B 44 53.552 16.429 9.553 1.00 45.51 ATOM 123 C GLY B 44 52.528 15.420 9.988 1.00 45.51 ATOM 124 O GLY B 44 52.715 14.724 10.988 1.00 45.51 ATOM 125 N GLY B 45 51.427 15.337 9.251 1.00 45.51 ATOM 126 CA GLY B 45 50.396 14.354 9.569 1.00 45.51 ATOM 127 C GLY B 45 50.151 13.441 8.371 1.00 45.51 ATOM 128 O GLY B 45 49.889 13.946 7.289 1.00 45.51 ATOM 129 N GLY B 46 50.245 12.121 8.536 1.00 45.51 ATOM 130 CA GLY B 46 49.931 11.168 7.466 1.00 45.51 ATOM 131 C GLY B 46 48.499 10.669 7.538 1.00 45.51 ATOM 132 O GLY B 46 48.034 10.247 8.603 1.00 45.51 ATOM 133 N GLY B 47 47.753 10.690 6.421 1.00 45.51 ATOM 134 CA GLY B 47 46.352 10.333 6.419 1.00 45.51 ATOM 135 C GLY B 47 46.093 9.205 5.423 1.00 45.51 ATOM 136 O GLY B 47 46.648 9.205 4.307 1.00 45.51 ATOM 137 N GLY C 51 59.494 -28.736 16.518 1.00 45.51 ATOM 138 CA GLY C 51 58.985 -27.399 16.806 1.00 45.51 ATOM 139 C GLY C 51 58.707 -26.740 15.458 1.00 45.51 ATOM 140 O GLY C 51 59.187 -27.203 14.402 1.00 45.51 ATOM 141 N GLY C 52 57.935 -25.663 15.452 1.00 45.51 ATOM 142 CA GLY C 52 57.542 -25.027 14.199 1.00 45.51 ATOM 143 C GLY C 52 57.918 -23.570 14.199 1.00 45.51 ATOM 144 O GLY C 52 57.638 -22.850 15.166 1.00 45.51 ATOM 145 N GLY C 53 58.591 -23.105 13.139 1.00 45.51 ATOM 146 CA GLY C 53 58.814 -21.669 13.001 1.00 45.51 ATOM 147 C GLY C 53 57.956 -21.201 11.828 1.00 45.51 ATOM 148 O GLY C 53 57.614 -21.954 10.905 1.00 45.51 ATOM 149 N GLY C 54 57.544 -19.937 11.888 1.00 45.51 ATOM 150 CA GLY C 54 56.633 -19.392 10.901 1.00 45.51 ATOM 151 C GLY C 54 57.024 -17.987 10.472 1.00 45.51 ATOM 152 O GLY C 54 57.877 -17.339 11.070 1.00 45.51 ATOM 153 N GLY C 55 56.412 -17.526 9.385 1.00 45.51 ATOM 154 CA GLY C 55 56.696 -16.207 8.845 1.00 45.51 ATOM 155 C GLY C 55 55.968 -16.006 7.530 1.00 45.51 ATOM 156 O GLY C 55 55.109 -16.788 7.123 1.00 45.51 ATOM 157 N GLY C 56 56.369 -14.940 6.838 1.00 45.51 ATOM 158 CA GLY C 56 55.784 -14.538 5.562 1.00 45.51 ATOM 159 C GLY C 56 56.871 -14.290 4.508 1.00 45.51 ATOM 160 O GLY C 56 57.827 -13.546 4.735 1.00 45.51 ATOM 161 N GLY C 57 56.706 -14.908 3.327 1.00 45.51 ATOM 162 CA GLY C 57 57.613 -14.750 2.194 1.00 45.51 ATOM 163 C GLY C 57 57.662 -13.318 1.661 1.00 45.51 ATOM 164 O GLY C 57 56.806 -12.493 1.982 1.00 45.51 ATOM 165 N GLY C 58 58.646 -13.053 0.793 1.00 45.51 ATOM 166 CA GLY C 58 58.854 -11.745 0.181 1.00 45.51 ATOM 167 C GLY C 58 57.629 -11.111 -0.475 1.00 45.51 ATOM 168 O GLY C 58 57.399 -9.902 -0.386 1.00 45.51 ATOM 169 N GLY C 59 56.811 -11.940 -1.124 1.00 45.51 ATOM 170 CA GLY C 59 55.624 -11.431 -1.772 1.00 45.51 ATOM 171 C GLY C 59 54.303 -11.837 -1.126 1.00 45.51 ATOM 172 O GLY C 59 53.279 -12.000 -1.795 1.00 45.51 ATOM 173 N GLY C 60 54.336 -12.000 0.209 1.00 45.51 ATOM 174 CA GLY C 60 53.124 -12.164 1.004 1.00 45.51 ATOM 175 C GLY C 60 52.671 -13.547 1.444 1.00 45.51 ATOM 176 O GLY C 60 51.856 -13.610 2.364 1.00 45.51 ATOM 177 N GLY C 61 53.122 -14.663 0.870 1.00 45.51 ATOM 178 CA GLY C 61 52.651 -15.991 1.265 1.00 45.51 ATOM 179 C GLY C 61 53.082 -16.427 2.680 1.00 45.51 ATOM 180 O GLY C 61 54.246 -16.269 3.045 1.00 45.51 ATOM 181 N GLY C 62 52.213 -16.984 3.533 1.00 45.51 ATOM 182 CA GLY C 62 52.606 -17.639 4.782 1.00 45.51 ATOM 183 C GLY C 62 53.407 -18.924 4.576 1.00 45.51 ATOM 184 O GLY C 62 53.219 -19.662 3.599 1.00 45.51 ATOM 185 N GLY C 63 54.348 -19.178 5.501 1.00 45.51 ATOM 186 CA GLY C 63 55.061 -20.454 5.503 1.00 45.51 ATOM 187 C GLY C 63 55.175 -20.959 6.924 1.00 45.51 ATOM 188 O GLY C 63 55.134 -20.181 7.886 1.00 45.51 ATOM 189 N GLY C 64 55.379 -22.269 7.006 1.00 45.51 ATOM 190 CA GLY C 64 55.657 -22.931 8.274 1.00 45.51 ATOM 191 C GLY C 64 56.729 -23.958 8.051 1.00 45.51 ATOM 192 O GLY C 64 56.681 -24.718 7.082 1.00 45.51 ATOM 193 N GLY C 65 57.717 -23.986 8.937 1.00 45.51 ATOM 194 CA GLY C 65 58.782 -24.980 8.829 1.00 45.51 ATOM 195 C GLY C 65 58.857 -25.811 10.107 1.00 45.51 ATOM 196 O GLY C 65 58.967 -25.235 11.179 1.00 45.51 ATOM 197 N GLY C 66 58.785 -27.140 10.016 1.00 45.51 ATOM 198 CA GLY C 66 58.945 -28.019 11.179 1.00 45.51 ATOM 199 C GLY C 66 60.372 -28.512 11.338 1.00 45.51 ATOM 200 O GLY C 66 60.980 -28.998 10.378 1.00 45.51 ATOM 201 N GLY C 67 60.957 -28.413 12.544 1.00 45.51 ATOM 202 CA GLY C 67 62.343 -28.758 12.763 1.00 45.51 ATOM 203 C GLY C 67 62.460 -29.818 13.856 1.00 45.51 ATOM 204 O GLY C 67 61.756 -29.750 14.882 1.00 45.51 ATOM 205 N GLY D 71 25.199 42.149 2.692 1.00 45.51 ATOM 206 CA GLY D 71 24.683 40.814 2.408 1.00 45.51 ATOM 207 C GLY D 71 24.408 40.159 3.758 1.00 45.51 ATOM 208 O GLY D 71 24.894 40.621 4.811 1.00 45.51 ATOM 209 N GLY D 72 23.631 39.085 3.768 1.00 45.51 ATOM 210 CA GLY D 72 23.239 38.453 5.024 1.00 45.51 ATOM 211 C GLY D 72 23.609 36.994 5.024 1.00 45.51 ATOM 212 O GLY D 72 23.322 36.273 4.060 1.00 45.51 ATOM 213 N GLY D 73 24.284 36.527 6.082 1.00 45.51 ATOM 214 CA GLY D 73 24.500 35.090 6.222 1.00 45.51 ATOM 215 C GLY D 73 23.645 34.628 7.398 1.00 45.51 ATOM 216 O GLY D 73 23.309 35.384 8.322 1.00 45.51 ATOM 217 N GLY D 74 23.226 33.366 7.342 1.00 45.51 ATOM 218 CA GLY D 74 22.317 32.827 8.333 1.00 45.51 ATOM 219 C GLY D 74 22.703 31.420 8.763 1.00 45.51 ATOM 220 O GLY D 74 23.551 30.768 8.163 1.00 45.51 ATOM 221 N GLY D 75 22.093 30.964 9.853 1.00 45.51 ATOM 222 CA GLY D 75 22.373 29.644 10.393 1.00 45.51 ATOM 223 C GLY D 75 21.649 29.449 11.711 1.00 45.51 ATOM 224 O GLY D 75 20.795 30.235 12.120 1.00 45.51 ATOM 225 N GLY D 76 22.048 28.382 12.403 1.00 45.51 ATOM 226 CA GLY D 76 21.465 27.984 13.682 1.00 45.51 ATOM 227 C GLY D 76 22.556 27.733 14.733 1.00 45.51 ATOM 228 O GLY D 76 23.507 26.985 14.503 1.00 45.51 ATOM 229 N GLY D 77 22.398 28.353 15.913 1.00 45.51 ATOM 230 CA GLY D 77 23.308 28.193 17.043 1.00 45.51 ATOM 231 C GLY D 77 23.353 26.762 17.577 1.00 45.51 ATOM 232 O GLY D 77 22.492 25.940 17.261 1.00 45.51 ATOM 233 N GLY D 78 24.339 26.494 18.443 1.00 45.51 ATOM 234 CA GLY D 78 24.543 25.185 19.056 1.00 45.51 ATOM 235 C GLY D 78 23.317 24.558 19.718 1.00 45.51 ATOM 236 O GLY D 78 23.082 23.350 19.631 1.00 45.51 ATOM 237 N GLY D 79 22.506 25.392 20.368 1.00 45.51 ATOM 238 CA GLY D 79 21.319 24.889 21.021 1.00 45.51 ATOM 239 C GLY D 79 19.998 25.300 20.380 1.00 45.51 ATOM 240 O GLY D 79 18.977 25.469 21.052 1.00 45.51 ATOM 241 N GLY D 80 20.026 25.461 19.044 1.00 45.51 ATOM 242 CA GLY D 80 18.812 25.629 18.253 1.00 45.51 ATOM 243 C GLY D 80 18.363 27.014 17.813 1.00 45.51 ATOM 244 O GLY D 80 17.545 27.079 16.896 1.00 45.51 ATOM 245 N GLY D 81 18.822 28.129 18.384 1.00 45.51 ATOM 246 CA GLY D 81 18.355 29.459 17.988 1.00 45.51 ATOM 247 C GLY D 81 18.783 29.890 16.571 1.00 45.51 ATOM 248 O GLY D 81 19.945 29.727 16.202 1.00 45.51 ATOM 249 N GLY D 82 17.913 30.451 15.720 1.00 45.51 ATOM 250 CA GLY D 82 18.305 31.101 14.469 1.00 45.51 ATOM 251 C GLY D 82 19.112 32.383 14.670 1.00 45.51 ATOM 252 O GLY D 82 18.932 33.124 15.647 1.00 45.51 ATOM 253 N GLY D 83 20.051 32.631 13.741 1.00 45.51 ATOM 254 CA GLY D 83 20.770 33.904 13.735 1.00 45.51 ATOM 255 C GLY D 83 20.881 34.406 12.312 1.00 45.51 ATOM 256 O GLY D 83 20.833 33.627 11.352 1.00 45.51 ATOM 257 N GLY D 84 21.091 35.715 12.228 1.00 45.51 ATOM 258 CA GLY D 84 21.367 36.374 10.959 1.00 45.51 ATOM 259 C GLY D 84 22.445 37.397 11.176 1.00 45.51 ATOM 260 O GLY D 84 22.404 38.159 12.144 1.00 45.51 ATOM 261 N GLY D 85 23.429 37.418 10.286 1.00 45.51 ATOM 262 CA GLY D 85 24.499 38.408 10.388 1.00 45.51 ATOM 263 C GLY D 85 24.573 39.237 9.110 1.00 45.51 ATOM 264 O GLY D 85 24.676 38.659 8.037 1.00 45.51 ATOM 265 N GLY D 86 24.507 40.566 9.199 1.00 45.51 ATOM 266 CA GLY D 86 24.667 41.443 8.034 1.00 45.51 ATOM 267 C GLY D 86 26.096 41.929 7.868 1.00 45.51 ATOM 268 O GLY D 86 26.709 42.414 8.826 1.00 45.51 ATOM 269 N GLY D 87 26.676 41.826 6.660 1.00 45.51 ATOM 270 CA GLY D 87 28.063 42.164 6.437 1.00 45.51 ATOM 271 C GLY D 87 28.181 43.222 5.341 1.00 45.51 ATOM 272 O GLY D 87 27.472 43.155 4.318 1.00 45.51 ATOM 273 N GLY E 91 28.742 29.848 62.009 1.00 45.51 ATOM 274 CA GLY E 91 29.268 28.524 62.325 1.00 45.51 ATOM 275 C GLY E 91 29.601 27.861 60.992 1.00 45.51 ATOM 276 O GLY E 91 29.146 28.306 59.917 1.00 45.51 ATOM 277 N GLY E 92 30.394 26.799 61.019 1.00 45.51 ATOM 278 CA GLY E 92 30.839 26.162 59.784 1.00 45.51 ATOM 279 C GLY E 92 30.491 24.697 59.784 1.00 45.51 ATOM 280 O GLY E 92 30.755 23.990 60.765 1.00 45.51 ATOM 281 N GLY E 93 29.862 24.211 58.707 1.00 45.51 ATOM 282 CA GLY E 93 29.672 22.770 58.574 1.00 45.51 ATOM 283 C GLY E 93 30.575 22.310 57.433 1.00 45.51 ATOM 284 O GLY E 93 30.932 23.063 56.514 1.00 45.51 ATOM 285 N GLY E 94 31.010 21.055 57.516 1.00 45.51 ATOM 286 CA GLY E 94 31.962 20.521 56.563 1.00 45.51 ATOM 287 C GLY E 94 31.613 19.105 56.133 1.00 45.51 ATOM 288 O GLY E 94 30.754 18.444 56.709 1.00 45.51 ATOM 289 N GLY E 95 32.268 18.648 55.070 1.00 45.51 ATOM 290 CA GLY E 95 32.027 17.319 54.532 1.00 45.51 ATOM 291 C GLY E 95 32.800 17.123 53.242 1.00 45.51 ATOM 292 O GLY E 95 33.656 17.919 52.857 1.00 45.51 ATOM 293 N GLY E 96 32.443 16.044 52.547 1.00 45.51 ATOM 294 CA GLY E 96 33.076 15.644 51.293 1.00 45.51 ATOM 295 C GLY E 96 32.027 15.367 50.207 1.00 45.51 ATOM 296 O GLY E 96 31.080 14.606 50.410 1.00 45.51 ATOM 297 N GLY E 97 32.218 15.979 49.027 1.00 45.51 ATOM 298 CA GLY E 97 31.351 15.794 47.868 1.00 45.51 ATOM 299 C GLY E 97 31.346 14.358 47.346 1.00 45.51 ATOM 300 O GLY E 97 32.208 13.552 47.700 1.00 45.51 ATOM 301 N GLY E 98 30.396 14.067 46.448 1.00 45.51 ATOM 302 CA GLY E 98 30.233 12.750 45.841 1.00 45.51 ATOM 303 C GLY E 98 31.491 12.136 45.229 1.00 45.51 ATOM 304 O GLY E 98 31.741 10.932 45.335 1.00 45.51 ATOM 305 N GLY E 99 32.312 12.976 44.600 1.00 45.51 ATOM 306 CA GLY E 99 33.529 12.486 43.993 1.00 45.51 ATOM 307 C GLY E 99 34.820 12.923 44.677 1.00 45.51 ATOM 308 O GLY E 99 35.862 13.101 44.040 1.00 45.51 ATOM 309 N GLY E 100 34.742 13.096 46.009 1.00 45.51 ATOM 310 CA GLY E 100 35.925 13.289 46.841 1.00 45.51 ATOM 311 C GLY E 100 36.337 14.685 47.284 1.00 45.51 ATOM 312 O GLY E 100 37.120 14.771 48.229 1.00 45.51 ATOM 313 N GLY E 101 35.882 15.787 46.687 1.00 45.51 ATOM 314 CA GLY E 101 36.314 17.127 47.086 1.00 45.51 ATOM 315 C GLY E 101 35.830 17.565 48.483 1.00 45.51 ATOM 316 O GLY E 101 34.658 17.387 48.812 1.00 45.51 ATOM 317 N GLY E 102 36.661 18.146 49.358 1.00 45.51 ATOM 318 CA GLY E 102 36.215 18.802 50.589 1.00 45.51 ATOM 319 C GLY E 102 35.396 20.070 50.347 1.00 45.51 ATOM 320 O GLY E 102 35.600 20.804 49.370 1.00 45.51 ATOM 321 N GLY E 103 34.421 20.311 51.240 1.00 45.51 ATOM 322 CA GLY E 103 33.684 21.573 51.208 1.00 45.51 ATOM 323 C GLY E 103 33.515 22.086 52.622 1.00 45.51 ATOM 324 O GLY E 103 33.540 21.317 53.591 1.00 45.51 ATOM 325 N GLY E 104 33.282 23.393 52.686 1.00 45.51 ATOM 326 CA GLY E 104 32.952 24.059 53.939 1.00 45.51 ATOM 327 C GLY E 104 31.867 25.063 53.674 1.00 45.51 ATOM 328 O GLY E 104 31.931 25.816 52.701 1.00 45.51 ATOM 329 N GLY E 105 30.851 25.077 54.528 1.00 45.51 ATOM 330 CA GLY E 105 29.772 26.049 54.379 1.00 45.51 ATOM 331 C GLY E 105 29.640 26.889 55.646 1.00 45.51 ATOM 332 O GLY E 105 29.507 26.319 56.719 1.00 45.51 ATOM 333 N GLY E 106 29.689 28.218 55.547 1.00 45.51 ATOM 334 CA GLY E 106 29.474 29.102 56.697 1.00 45.51 ATOM 335 C GLY E 106 28.033 29.568 56.807 1.00 45.51 ATOM 336 O GLY E 106 27.447 30.035 55.824 1.00 45.51 ATOM 337 N GLY E 107 27.413 29.467 57.995 1.00 45.51 ATOM 338 CA GLY E 107 26.014 29.786 58.166 1.00 45.51 ATOM 339 C GLY E 107 25.841 30.852 59.247 1.00 45.51 ATOM 340 O GLY E 107 26.514 30.805 60.295 1.00 45.51 ATOM 341 N GLY F 111 40.788 -8.794 48.156 1.00 45.51 ATOM 342 CA GLY F 111 40.376 -10.101 47.653 1.00 45.51 ATOM 343 C GLY F 111 39.900 -10.901 48.862 1.00 45.51 ATOM 344 O GLY F 111 40.184 -10.544 50.025 1.00 45.51 ATOM 345 N GLY F 112 39.172 -11.984 48.629 1.00 45.51 ATOM 346 CA GLY F 112 38.597 -12.753 49.728 1.00 45.51 ATOM 347 C GLY F 112 39.015 -14.196 49.644 1.00 45.51 ATOM 348 O GLY F 112 38.921 -14.816 48.577 1.00 45.51 ATOM 349 N GLY F 113 39.517 -14.760 50.750 1.00 45.51 ATOM 350 CA GLY F 113 39.759 -16.199 50.778 1.00 45.51 ATOM 351 C GLY F 113 38.734 -16.800 51.737 1.00 45.51 ATOM 352 O GLY F 113 38.220 -16.152 52.661 1.00 45.51 ATOM 353 N GLY F 114 38.378 -18.056 51.481 1.00 45.51 ATOM 354 CA GLY F 114 37.334 -18.714 52.242 1.00 45.51 ATOM 355 C GLY F 114 37.693 -20.151 52.586 1.00 45.51 ATOM 356 O GLY F 114 38.653 -20.720 52.078 1.00 45.51 ATOM 357 N GLY F 115 36.924 -20.732 53.503 1.00 45.51 ATOM 358 CA GLY F 115 37.157 -22.096 53.947 1.00 45.51 ATOM 359 C GLY F 115 36.228 -22.444 55.095 1.00 45.51 ATOM 360 O GLY F 115 35.289 -21.721 55.428 1.00 45.51 ATOM 361 N GLY F 116 36.542 -23.570 55.733 1.00 45.51 ATOM 362 CA GLY F 116 35.767 -24.113 56.846 1.00 45.51 ATOM 363 C GLY F 116 36.672 -24.454 58.037 1.00 45.51 ATOM 364 O GLY F 116 37.675 -25.156 57.900 1.00 45.51 ATOM 365 N GLY F 117 36.294 -23.965 59.230 1.00 45.51 ATOM 366 CA GLY F 117 37.006 -24.228 60.477 1.00 45.51 ATOM 367 C GLY F 117 37.011 -25.707 60.863 1.00 45.51 ATOM 368 O GLY F 117 36.247 -26.506 60.322 1.00 45.51 ATOM 369 N GLY F 118 37.846 -26.047 61.854 1.00 45.51 ATOM 370 CA GLY F 118 37.991 -27.409 62.357 1.00 45.51 ATOM 371 C GLY F 118 36.695 -28.125 62.731 1.00 45.51 ATOM 372 O GLY F 118 36.521 -29.322 62.483 1.00 45.51 ATOM 373 N GLY F 119 35.755 -27.381 63.313 1.00 45.51 ATOM 374 CA GLY F 119 34.494 -27.972 63.699 1.00 45.51 ATOM 375 C GLY F 119 33.286 -27.520 62.884 1.00 45.51 ATOM 376 O GLY F 119 32.161 -27.442 63.385 1.00 45.51 ATOM 377 N GLY F 120 33.534 -27.217 61.597 1.00 45.51 ATOM 378 CA GLY F 120 32.466 -26.988 60.630 1.00 45.51 ATOM 379 C GLY F 120 32.048 -25.573 60.262 1.00 45.51 ATOM 380 O GLY F 120 31.395 -25.426 59.229 1.00 45.51 ATOM 381 N GLY F 121 32.362 -24.517 61.013 1.00 45.51 ATOM 382 CA GLY F 121 31.921 -23.162 60.680 1.00 45.51 ATOM 383 C GLY F 121 32.567 -22.575 59.409 1.00 45.51 ATOM 384 O GLY F 121 33.780 -22.676 59.230 1.00 45.51 ATOM 385 N GLY F 122 31.834 -21.943 58.483 1.00 45.51 ATOM 386 CA GLY F 122 32.407 -21.156 57.390 1.00 45.51 ATOM 387 C GLY F 122 33.122 -19.888 57.856 1.00 45.51 ATOM 388 O GLY F 122 32.752 -19.259 58.857 1.00 45.51 ATOM 389 N GLY F 123 34.195 -19.525 57.132 1.00 45.51 ATOM 390 CA GLY F 123 34.857 -18.246 57.379 1.00 45.51 ATOM 391 C GLY F 123 35.189 -17.594 56.055 1.00 45.51 ATOM 392 O GLY F 123 35.333 -18.267 55.026 1.00 45.51 ATOM 393 N GLY F 124 35.363 -16.279 56.141 1.00 45.51 ATOM 394 CA GLY F 124 35.825 -15.484 55.012 1.00 45.51 ATOM 395 C GLY F 124 36.812 -14.471 55.514 1.00 45.51 ATOM 396 O GLY F 124 36.581 -13.817 56.532 1.00 45.51 ATOM 397 N GLY F 125 37.932 -14.337 54.813 1.00 45.51 ATOM 398 CA GLY F 125 38.932 -13.344 55.197 1.00 45.51 ATOM 399 C GLY F 125 39.191 -12.382 54.041 1.00 45.51 ATOM 400 O GLY F 125 39.496 -12.841 52.950 1.00 45.51 ATOM 401 N GLY F 126 39.063 -11.072 54.252 1.00 45.51 ATOM 402 CA GLY F 126 39.386 -10.074 53.227 1.00 45.51 ATOM 403 C GLY F 126 40.803 -9.546 53.360 1.00 45.51 ATOM 404 O GLY F 126 41.228 -9.155 54.453 1.00 45.51 ATOM 405 N GLY F 127 41.582 -9.510 52.266 1.00 45.51 ATOM 406 CA GLY F 127 42.974 -9.124 52.319 1.00 45.51 ATOM 407 C GLY F 127 43.237 -7.953 51.373 1.00 45.51 ATOM 408 O GLY F 127 42.715 -7.924 50.242 1.00 45.51 ATOM 409 N GLY G 131 75.299 -2.784 62.188 1.00 45.51 ATOM 410 CA GLY G 131 74.881 -1.484 62.702 1.00 45.51 ATOM 411 C GLY G 131 74.405 -0.675 61.499 1.00 45.51 ATOM 412 O GLY G 131 74.692 -1.020 60.334 1.00 45.51 ATOM 413 N GLY G 132 73.672 0.403 61.740 1.00 45.51 ATOM 414 CA GLY G 132 73.096 1.179 60.647 1.00 45.51 ATOM 415 C GLY G 132 73.508 2.624 60.745 1.00 45.51 ATOM 416 O GLY G 132 73.410 3.233 61.818 1.00 45.51 ATOM 417 N GLY G 133 74.011 3.200 59.645 1.00 45.51 ATOM 418 CA GLY G 133 74.247 4.640 59.631 1.00 45.51 ATOM 419 C GLY G 133 73.222 5.245 58.675 1.00 45.51 ATOM 420 O GLY G 133 72.712 4.604 57.744 1.00 45.51 ATOM 421 N GLY G 134 72.860 6.498 58.941 1.00 45.51 ATOM 422 CA GLY G 134 71.816 7.159 58.185 1.00 45.51 ATOM 423 C GLY G 134 72.169 8.600 57.854 1.00 45.51 ATOM 424 O GLY G 134 73.127 9.168 58.370 1.00 45.51 ATOM 425 N GLY G 135 71.400 9.186 56.941 1.00 45.51 ATOM 426 CA GLY G 135 71.628 10.555 56.510 1.00 45.51 ATOM 427 C GLY G 135 70.700 10.910 55.364 1.00 45.51 ATOM 428 O GLY G 135 69.765 10.186 55.022 1.00 45.51 ATOM 429 N GLY G 136 71.012 12.043 54.737 1.00 45.51 ATOM 430 CA GLY G 136 70.236 12.592 53.627 1.00 45.51 ATOM 431 C GLY G 136 71.143 12.947 52.441 1.00 45.51 ATOM 432 O GLY G 136 72.143 13.652 52.586 1.00 45.51 ATOM 433 N GLY G 137 70.769 12.468 51.243 1.00 45.51 ATOM 434 CA GLY G 137 71.482 12.745 50.000 1.00 45.51 ATOM 435 C GLY G 137 71.483 14.227 49.627 1.00 45.51 ATOM 436 O GLY G 137 70.714 15.018 50.174 1.00 45.51 ATOM 437 N GLY G 138 72.317 14.579 48.641 1.00 45.51 ATOM 438 CA GLY G 138 72.459 15.946 48.151 1.00 45.51 ATOM 439 C GLY G 138 71.160 16.661 47.781 1.00 45.51 ATOM 440 O GLY G 138 70.982 17.855 48.039 1.00 45.51 ATOM 441 N GLY G 139 70.225 15.918 47.190 1.00 45.51 ATOM 442 CA GLY G 139 68.962 16.508 46.808 1.00 45.51 ATOM 443 C GLY G 139 67.754 16.044 47.615 1.00 45.51 ATOM 444 O GLY G 139 66.630 15.967 47.112 1.00 45.51 ATOM 445 N GLY G 140 68.001 15.731 48.900 1.00 45.51 ATOM 446 CA GLY G 140 66.932 15.489 49.863 1.00 45.51 ATOM 447 C GLY G 140 66.519 14.069 50.218 1.00 45.51 ATOM 448 O GLY G 140 65.864 13.911 51.247 1.00 45.51 ATOM 449 N GLY G 141 66.839 13.021 49.457 1.00 45.51 ATOM 450 CA GLY G 141 66.402 11.661 49.777 1.00 45.51 ATOM 451 C GLY G 141 67.048 11.065 51.044 1.00 45.51 ATOM 452 O GLY G 141 68.260 11.170 51.226 1.00 45.51 ATOM 453 N GLY G 142 66.315 10.423 51.963 1.00 45.51 ATOM 454 CA GLY G 142 66.889 9.628 53.050 1.00 45.51 ATOM 455 C GLY G 142 67.610 8.367 52.574 1.00 45.51 ATOM 456 O GLY G 142 67.244 7.745 51.566 1.00 45.51 ATOM 457 N GLY G 143 68.683 8.002 53.297 1.00 45.51 ATOM 458 CA GLY G 143 69.350 6.727 53.039 1.00 45.51 ATOM 459 C GLY G 143 69.682 6.064 54.358 1.00 45.51 ATOM 460 O GLY G 143 69.821 6.729 55.393 1.00 45.51 ATOM 461 N GLY G 144 69.861 4.751 54.260 1.00 45.51 ATOM 462 CA GLY G 144 70.324 3.948 55.384 1.00 45.51 ATOM 463 C GLY G 144 71.316 2.943 54.874 1.00 45.51 ATOM 464 O GLY G 144 71.089 2.297 53.850 1.00 45.51 ATOM 465 N GLY G 145 72.435 2.806 55.576 1.00 45.51 ATOM 466 CA GLY G 145 73.439 1.821 55.184 1.00 45.51 ATOM 467 C GLY G 145 73.700 0.850 56.332 1.00 45.51 ATOM 468 O GLY G 145 74.000 1.301 57.428 1.00 45.51 ATOM 469 N GLY G 146 73.577 -0.459 56.109 1.00 45.51 ATOM 470 CA GLY G 146 73.902 -1.465 57.126 1.00 45.51 ATOM 471 C GLY G 146 75.321 -1.986 56.991 1.00 45.51 ATOM 472 O GLY G 146 75.749 -2.366 55.895 1.00 45.51 ATOM 473 N GLY G 147 76.098 -2.029 58.087 1.00 45.51 ATOM 474 CA GLY G 147 77.492 -2.410 58.032 1.00 45.51 ATOM 475 C GLY G 147 77.757 -3.587 58.968 1.00 45.51 ATOM 476 O GLY G 147 77.233 -3.628 60.098 1.00 45.51 ATOM 477 N GLY H 151 63.195 -41.496 48.742 1.00 45.51 ATOM 478 CA GLY H 151 63.714 -40.174 48.407 1.00 45.51 ATOM 479 C GLY H 151 64.044 -39.490 49.730 1.00 45.51 ATOM 480 O GLY H 151 63.591 -39.921 50.811 1.00 45.51 ATOM 481 N GLY H 152 64.831 -38.424 49.688 1.00 45.51 ATOM 482 CA GLY H 152 65.274 -37.768 50.914 1.00 45.51 ATOM 483 C GLY H 152 64.919 -36.305 50.891 1.00 45.51 ATOM 484 O GLY H 152 65.179 -35.611 49.900 1.00 45.51 ATOM 485 N GLY H 153 64.287 -35.805 51.961 1.00 45.51 ATOM 486 CA GLY H 153 64.090 -34.364 52.073 1.00 45.51 ATOM 487 C GLY H 153 64.991 -33.883 53.207 1.00 45.51 ATOM 488 O GLY H 153 65.351 -34.621 54.137 1.00 45.51 ATOM 489 N GLY H 154 65.420 -32.627 53.106 1.00 45.51 ATOM 490 CA GLY H 154 66.369 -32.075 54.052 1.00 45.51 ATOM 491 C GLY H 154 66.013 -30.654 54.460 1.00 45.51 ATOM 492 O GLY H 154 65.151 -30.007 53.874 1.00 45.51 ATOM 493 N GLY H 155 66.666 -30.179 55.517 1.00 45.51 ATOM 494 CA GLY H 155 66.418 -28.844 56.035 1.00 45.51 ATOM 495 C GLY H 155 67.190 -28.625 57.322 1.00 45.51 ATOM 496 O GLY H 155 68.050 -29.411 57.719 1.00 45.51 ATOM 497 N GLY H 156 66.827 -27.538 58.001 1.00 45.51 ATOM 498 CA GLY H 156 67.458 -27.116 59.249 1.00 45.51 ATOM 499 C GLY H 156 66.408 -26.828 60.330 1.00 45.51 ATOM 500 O GLY H 156 65.457 -26.075 60.117 1.00 45.51 ATOM 501 N GLY H 157 66.602 -27.422 61.520 1.00 45.51 ATOM 502 CA GLY H 157 65.733 -27.224 62.676 1.00 45.51 ATOM 503 C GLY H 157 65.722 -25.781 63.177 1.00 45.51 ATOM 504 O GLY H 157 66.580 -24.976 62.812 1.00 45.51 ATOM 505 N GLY H 158 64.770 -25.481 64.070 1.00 45.51 ATOM 506 CA GLY H 158 64.600 -24.156 64.658 1.00 45.51 ATOM 507 C GLY H 158 65.855 -23.527 65.261 1.00 45.51 ATOM 508 O GLY H 158 66.100 -22.324 65.137 1.00 45.51 ATOM 509 N GLY H 159 66.681 -24.354 65.902 1.00 45.51 ATOM 510 CA GLY H 159 67.895 -23.849 66.502 1.00 45.51 ATOM 511 C GLY H 159 69.189 -24.290 65.825 1.00 45.51 ATOM 512 O GLY H 159 70.231 -24.454 66.465 1.00 45.51 ATOM 513 N GLY H 160 69.112 -24.482 64.495 1.00 45.51 ATOM 514 CA GLY H 160 70.295 -24.683 63.666 1.00 45.51 ATOM 515 C GLY H 160 70.714 -26.083 63.244 1.00 45.51 ATOM 516 O GLY H 160 71.499 -26.178 62.301 1.00 45.51 ATOM 517 N GLY H 161 70.265 -27.178 63.858 1.00 45.51 ATOM 518 CA GLY H 161 70.704 -28.522 63.478 1.00 45.51 ATOM 519 C GLY H 161 70.221 -28.982 62.088 1.00 45.51 ATOM 520 O GLY H 161 69.048 -28.815 61.755 1.00 45.51 ATOM 521 N GLY H 162 71.055 -29.572 61.221 1.00 45.51 ATOM 522 CA GLY H 162 70.613 -30.248 60.001 1.00 45.51 ATOM 523 C GLY H 162 69.800 -31.516 60.260 1.00 45.51 ATOM 524 O GLY H 162 70.007 -32.235 61.248 1.00 45.51 ATOM 525 N GLY H 163 68.826 -31.775 59.371 1.00 45.51 ATOM 526 CA GLY H 163 68.095 -33.040 59.421 1.00 45.51 ATOM 527 C GLY H 163 67.928 -33.575 58.016 1.00 45.51 ATOM 528 O GLY H 163 67.951 -32.820 57.035 1.00 45.51 ATOM 529 N GLY H 164 67.702 -34.883 57.970 1.00 45.51 ATOM 530 CA GLY H 164 67.375 -35.569 56.728 1.00 45.51 ATOM 531 C GLY H 164 66.295 -36.574 57.007 1.00 45.51 ATOM 532 O GLY H 164 66.363 -37.313 57.991 1.00 45.51 ATOM 533 N GLY H 165 65.280 -36.606 56.153 1.00 45.51 ATOM 534 CA GLY H 165 64.205 -37.580 56.316 1.00 45.51 ATOM 535 C GLY H 165 64.077 -38.439 55.061 1.00 45.51 ATOM 536 O GLY H 165 63.942 -37.886 53.980 1.00 45.51 ATOM 537 N GLY H 166 64.132 -39.766 55.180 1.00 45.51 ATOM 538 CA GLY H 166 63.922 -40.669 54.043 1.00 45.51 ATOM 539 C GLY H 166 62.484 -41.142 53.940 1.00 45.51 ATOM 540 O GLY H 166 61.900 -41.598 54.930 1.00 45.51 ATOM 541 N GLY H 167 61.863 -41.062 52.750 1.00 45.51 ATOM 542 CA GLY H 167 60.465 -41.390 52.583 1.00 45.51 ATOM 543 C GLY H 167 60.298 -42.473 51.518 1.00 45.51 ATOM 544 O GLY H 167 60.971 -42.438 50.470 1.00 45.51

1 0

Support for KNIME?
by Schubert, Carsten [PRDUS] 24 Oct '07

24 Oct '07

Hi, I was wondering if anybody has looked into integrating phenix with KNIME (http://www.knime.org/), as part of a pipeline for structure solution. Is this something the developers have looked into? Cheers, Carsten

2 1

problems with map quality, refinement and R/Rfree
by Joe Smith 19 Oct '07

19 Oct '07

Hi all, We have data sets for a protein-RNA complex at 3.2 A resolution. . The data belong to the space group I4122 and contains one molecule of Protein-RNA complex (300AA and 16nt; 66% solvent content) in the asym unit. We have managed to get phases using Se-SAD and the present model contains 60% of the protein atoms (250 residues many of them build as Ala) and almost complete RNA (16nt). We could not locate ~20 % of the residues (present in various loops as well as at N- and C-terminal ends). First 120 residues present at N-terminal end seem to have poor relatively main-chain density and almost no side chain density. RNA and 130 residues present at the C-terminal end have good electron density for main-chain as well as side chain. The solution seems to be correct as molecular replacement trials with this model gave same solution in Phaser, Molrep and AMoRe. Solution seems to be also correct because as expected one RNA strand present in asym unit pairs with another one coming from symmetry related molecule. We have checked data in space group I4122 with CCP4 (SFCHECK, cumulative intensity distribution), Yeates server as well as Phenix.xtriage. In all the cases it indicates no twinning. However if I process the data in lower symmetry space group it does indicate presence of almost perfect twin. We realize that this could be just because of processing data in lower symmetry space group and data in all probability may still be fine. The problem is now with refinement and model building. Refinement with CNS and Refamc gave considerably higher value of R and R free. In CNS1.1, refinement with small changes in the model some time leads to large shift in R and R-free value. Refmac: R=36; Rfree=47 CNS1.1: R=40-59; R-free=45-63 However in both the cases map looks more or less same (with reasonably good density for the main-chain as well as RNA) I tried refining with phenix.refine and there is some improvement in the R(34%) and Rfree(40%) values. I think may be robust bulk solvent correction incorporated in phenix.refine has helped in this case. However, I still see no improvement in the map quality for the first 120 residues. In the absence of any clear density I am unable to build any further. I feel N-terminal domain is bit flexible and may have overall poor density. I have used Se position as well as predicted secondary structure in assigning the amino acid in the map but due to few breaks in the N-terminal domain as well as poor density I am unable to assign any amino acid into the poly ala main chain. Frankly speaking, I do not know how to proceed further. I welcome any kind of suggestions which could help us in this case. Regards Joe

1 0

1.3 beta rc3 version FC2 gui error
by Balasundaresan 12 Oct '07

12 Oct '07

Dear Author, I downloaded and installed the 1.3 beta rc3 version(GUI) in FEDORA CORE 2.0 and everything went well during installation and sourced it in .cshrc. while typing phenix in the command line I faced the below error, Traceback (most recent call last): File "/usr/local/phenix-1.3b-rc3/phenix/wxGUI/wxPhenix.py", line 11, in <module> import wx File "/usr/local/phenix-1.3b-rc3/build/intel-linux-2.6/base/lib/python2.5/site-packages/wx-2.8-gtk2-ansi/wx/__init__.py", line 45, in <module> from wx._core import * File "/usr/local/phenix-1.3b-rc3/build/intel-linux-2.6/base/lib/python2.5/site-packages/wx-2.8-gtk2-ansi/wx/_core.py", line 4, in <module> import _core_ ImportError: libstdc++.so.6: cannot open shared object file: No such file or directory any opinion or suggestions are welcome... regards Bala -- Balasundaresan <d-bala(a)aist.go.jp>

3 2

phenix.refine python error !!
by john kryst 12 Oct '07

12 Oct '07

Hi all !!! I have recently updated phenix version to phenix-1.3b-rc3. After that when i run phenix.refine it runs properly. But while writing the pdb file it is giving the following error. Traceback (most recent call last): File "/usr/local/phenix-1.3b-rc3/phenix/phenix/command_line/refine.py", line 5, in <module> command_line.run(command_name="phenix.refine", args=sys.argv[1:]) File "/usr/local/phenix-1.3b-rc3/phenix/phenix/refinement/command_line.py", line 89, in run refine_object.write_refined_pdb(f_pdb) File "/usr/local/phenix-1.3b-rc3/phenix/phenix/refinement/driver.py", line 1101, in write_refined_pdb pdb_header.write_remark_3(info = m_info, out = f) File "/usr/local/phenix-1.3b-rc3/mmtbx/mmtbx/pdb_header.py", line 21, in write_remark_3 info.show_remark_3(out = out) File "/usr/local/phenix-1.3b-rc3/mmtbx/mmtbx/model_statistics.py", line 483, in show_remark_3 self.data_x.show_remark_3(out = out) File "/usr/local/phenix-1.3b-rc3/mmtbx/mmtbx/f_model.py", line 2034, in show_remark_3 bin.n_work, bin.n_free, bin.r_work*100., bin.r_free*100.) TypeError: unsupported operand type(s) for *: 'NoneType' and 'float' I am using fedora 5, python 2.4.2. I have used phenix-installer-1.3b-rc3-intel-linux-2.4.tar. It was working fine in the last build. Google'ing the error didn't help much. Thanks for your inputs. regards John

2 1

Hires input file problem
by Troy E Messick 11 Oct '07

11 Oct '07

Hi all, I seem to be having a problem specifying the labels for the Hires dataset for an Autobuild run. Here is my input script: input_data_file sharp.mtz input_labels 'Fdm' 'SIGFPsha' 'PHIdm' 'FOMdm' 'HLAdm' 'HLBdm' 'HLCdm' 'HLDdm' 'FreeR_flag' input_pdb_file ab.pdb input_seq_file seq.dat input_hires_file output.native.sca Here is the error from the AutoBuild.log file: ************************************************************ Failed to carry out AutoBuild_datafile_info_inputs: 'all_input_hires_labels' ************************************************************ I've tried to use the mtz file from the ImportRawData_run directory and specify the columns by substituting the last line in my input script file with: input_hires_file output_PHX.mtz input_hires_labels 'output.native' 'SIGoutput.native' which are the only labels I could find from mtzdump and that doesn't work either. What am I missing here? Any suggestions would be greatly appreciated. Thanks, Troy

5 4

"Aromatic" question
by Claudia Scotti 10 Oct '07

10 Oct '07

Dear list, I've refined a protein at 2.0 A resolution with its ligand, a small molecule which includes a phenyl group. For this, I used elbow to generate the cif file, and in this file the atoms of the phenyl ring are correctly defined as "aromatic". However, the pdb output of the refinement shows a boat configuration for the 6 carbon atoms ring, with a very nice fit to the electron density. This would suggest a flexible cyclohexyl- substituent instead of the expected, typically planar phenyl ring. As my chemistry is poor, I'd really need some suggestions on where I'm wrong: did I give the wrong cif file or does phenix recognise a better fitting in a boat structure, indicating that my ligand phenyl moiety has been reduced somehow to a cyclohexyl one? Or is the aromatic ring of the phenyl group not so planar as I've supposed it to be until now? Any help would be very appreciated. Many many thanks, Claudia Claudia Scotti Dipartimento di Medicina Sperimentale Sezione di Patologia Generale Universita' di Pavia Piazza Botta, 10 27100 Pavia Italia Tel. 0039 0382 986335/8/1 Facs 0039 0382 303673 _________________________________________________________________ Connect to the next generation of MSN Messenger http://imagine-msn.com/messenger/launch80/default.aspx?locale=en-us&source=…

5 6

Confused with ANAISOU in PDB
by Partha Chakrabarti 09 Oct '07

09 Oct '07

Hi, I am bit confused with two things. First I did specify individual isotopic, as following, still see ANAISOU in PDB. Is it from TLS strategy? I have used TLS in refmac, don't see it there. Second thing is, I want to tighten the water picking. How can I do that? adp { individual { isotropic = "all" anisotropic = None } group = None one_adp_group_per_residue = True tls = "chain A" tls = "chain B" Best, Partha -- MRC National Institute for Medical Research Division of Molecular Structure The Ridgeway, NW7 1AA, UK Email: pchakra(a)nimr.mrc.ac.uk Phone: + 44 208 816 2515

2 5

planarities definition help
by Francis E Reyes 09 Oct '07

09 Oct '07

I need to specify a group of residues/atoms that must exist on the same plane for refinement. I think the keyword is refinement.geometry_restraints.planarities may be the right keyword, but I'm unsure as to the syntax for defining the selection? Thanks FR --------------------------------------------- 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

3 6

R free set in twinned dataset
by Jianghai Zhu 08 Oct '07

08 Oct '07

Hi, Can I use phenix.refine to generate R-free flag in the case of twinning? Will phenix.refine consider the twinning operator in the process? I couldn't find this information in the manual. Thanks. Jianghai +++++++++++++++++++++++++++++++ Jianghai Zhu, Ph.D CBR Institute for Biomedical Research Department of Pathology Harvard Medical School 200 Longwood Ave., Boston, MA 02115 Ph: 617-278-3211 Fx: 618-278-3232 +++++++++++++++++++++++++++++++

3 8

NAG-ASN link
by Jianghai Zhu 07 Oct '07

07 Oct '07

Hi, I got the following error when I added a NAG-ASN link in the def file. /nfs/home/jzhu/xiao/x61b/phenix6/temp/x61b.pdb Monomer Library directory: "/nfs/home/jzhu/phenix-1.3b-rc3/ext_ref_files/mon_lib" Total number of atoms: 46651 apply_cif_link: data_link: NAG-ASN mod_id_1: DEL-O1 mod_id_2: DEL-HD22 residue_selection_1: chain S and resname NAG and resid 1001 residue_selection_2: chain A and resname ASN and resid 15 Number of models: 1 Model: 0 Number of conformers: 1 Conformer: " " Number of atoms: 46651 Number of chains: 8 Number of residues, atoms: 909, 13713 Unexpected atoms: {'ASN%DEL-HD22,HD22': 1} Classifications: {'peptide': 909} Modifications used: {'DEL-HD22': 1, 'NH3': 1} Link IDs: {'PTRANS': 59, 'TRANS': 847, 'PCIS': 2} Chain breaks: 3 Number of residues, atoms: 601, 8947 Classifications: {'peptide': 601} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 28, 'TRANS': 569, 'PCIS': 3} Chain breaks: 2 Number of residues, atoms: 898, 13559 Classifications: {'peptide': 898} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 59, 'TRANS': 836, 'PCIS': 2} Chain breaks: 3 Number of residues, atoms: 602, 8954 Classifications: {'peptide': 602} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 28, 'TRANS': 570, 'PCIS': 3} Chain breaks: 2 Number of residues, atoms: 642, 642 Classifications: {'water': 642} Link IDs: {None: 641} Number of residues, atoms: 31, 780 Unusual residues: {'MAN': 7, 'NAG%DEL-O1': 1, 'NAG': 23} Classifications: {'undetermined': 31} Modifications used: {'DEL-O1': 1} Link IDs: {None: 30, 'NAG-ASN': 1} Unresolved non-hydrogen bonds: 30 Unresolved non-hydrogen angles: 60 Unresolved non-hydrogen chiralities: 30 Number of residues, atoms: 16, 16 Unusual residues: {' MG': 2, ' CA': 14} Classifications: {'undetermined': 16} Link IDs: {None: 15} Number of residues, atoms: 4, 40 Unusual residues: {'IMD': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Number of atoms with unknown nonbonded energy type symbols: 1 "HD22 ASN A 15 " Time building chain proxies: 32.54, per 1000 atoms: 0.70 Sorry: Fatal problems interpreting PDB file: Number of atoms with unknown nonbonded energy type symbols: 1 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. Couldn't figure out what went wrong. Can somebody help me? Thanks. Jianghai +++++++++++++++++++++++++++++++ Jianghai Zhu, Ph.D CBR Institute for Biomedical Research Department of Pathology Harvard Medical School 200 Longwood Ave., Boston, MA 02115 Ph: 617-278-3211 Fx: 618-278-3232 +++++++++++++++++++++++++++++++

2 7

twin fraction
by Jianghai Zhu 06 Oct '07

06 Oct '07

Hi, I am using the phenix 1.3 beta rc3 to refine a twinned structure. In the old version, phenix.refine would report a twin fraction for each cycle of refinement. I could not find the twin fraction anymore in either the log file or the output pdb file. Where is it now? Thanks. Jianghai +++++++++++++++++++++++++++++++ Jianghai Zhu, Ph.D CBR Institute for Biomedical Research Department of Pathology Harvard Medical School 200 Longwood Ave., Boston, MA 02115 Ph: 617-278-3211 Fx: 618-278-3232 +++++++++++++++++++++++++++++++

2 1

Hinge movement for refine?
by Partha Chakrabarti 04 Oct '07

04 Oct '07

Hiya, I have used rigid body refinement in phenix.refine as suggested: refinement.refine.sites { rigid_body = chain A rigid_body = chain B } If I have a multidomain protein like kinases, or G proteins which have flexible switches, how can I define the region within a given chain? Best, Partha -- MRC National Institute for Medical Research Division of Molecular Structure The Ridgeway, NW7 1AA, UK Email: pchakra(a)nimr.mrc.ac.uk Phone: + 44 208 816 2515

2 1

Re: [phenixbb] Question about strategy in phenix.refine
by Pavel Afonine 04 Oct '07

04 Oct '07

Hi, this figure from phenix.refine manual illustrates the refinement protocol the best (although it's a bit sketchy): http://phenix-online.org/documentation/refinement.htm#anch8 Pavel. > 2007/10/4, Partha Chakrabarti <ppchak(a)gmail.com>: > >> I am just trying to figure out certain details. For example, if one chooses >> multiple options in the strategies, how does the program decide if step 1 >> is nearly done and it can go to step 2? Of course I guess the whole process >> is iterative (macro cycle?) but having a bit control so to say.. >>

1 0

Question about strategy in phenix.refine
by Partha Chakrabarti 04 Oct '07

04 Oct '07

Hiya, I am wondering what is the meaning of the * in the following: strategy = *individual_sites rigid_body *individual_adp group_adp tls \ individual_occupancies group_occupancies group_anomalous none Does it mean, that this option can be used (for example for high res) but not used as default? Maybe I missed it, how can i get the cif files for ligands? Refmac generates it in several cases, can that be used? Regards, Partha -- MRC National Institute for Medical Research Division of Molecular Structure The Ridgeway, NW7 1AA, UK Email: pchakra(a)nimr.mrc.ac.uk Phone: + 44 208 816 2515

2 1

Team Leader vacancy: PX group, SGC-Oxford
by Frank von Delft 01 Oct '07

01 Oct '07

I have a vacancy for Team Leader for Infrastructure and Methods Development in my group that is still being advertised; this is the Protein Crystallography group of the Structural Genomics Consortium, Oxford. For details, please see: http://www.sgc.ox.ac.uk/jobs/07079.html, and feel free to contact me if curious. The remit of the Structural Genomics Consortium (SGC) is to solve human proteins of medical relevance and place them in the public domain without restrictions; it is funded by a consortium of public and industrial funders, and has independently operating sites in Oxford and Toronto Universities and Karolinska Institutet (Stockholm). The Oxford site solved nearly 200 such structures in its first three years, and has now entered Phase II, with 4 years of funding till June 2011; it now has an increased emphasis on chemical biology and membrane proteins. The Protein Crystallography group collaborates tightly with the 5 other groups to get their purified proteins crystallized and solved -- five per month, to be precise. Equally importantly, with all the robotics and toys you'd care for, and access not only to lots of real-life samples but also to 3 years' worth of structured data accumulated during Phase I, we're ideally positioned for development and testing of crystallographic methods, which will be the major scientific thrust of the group in this phase. Enthusiastic crystallographers, especially those that really enjoy the nuts and bolts of the technique and mucking around with tricks and toys, both crystallization and algorithms, are encouraged to apply. Frank von Delft Principal Investigator: Protein Crystallography Structural Genomics Consortium Oxford University, UK

1 0

Request for C shell script file for phenix.refine
by Partha Chakrabarti 01 Oct '07

01 Oct '07

Hi, I am wondering if one can have master scripts (C shell) for the macro cycle of phenix.refine that can be used from the command line. It is easier to comment out an option than having to type the whole thing.. has anybody tried it? Similar scripts exist for solve/resolve and phaser.. I should not say it, I am myself not adverse to using the GUI, it is just easier when the poor postdoc sits with the boss.. typically I face the question: where is the script file & where is the log file :)) Cheers, Partha -- MRC National Institute for Medical Research Division of Molecular Structure The Ridgeway, NW7 1AA, UK Email: pchakra(a)nimr.mrc.ac.uk Phone: + 44 208 816 2515

3 4

unintellible font
by Michael Sawaya 30 Sep '07

30 Sep '07

Dear Phenixbb, My recent installation of Phenix completed successfully, but the font in the Phenix graphics window is replaced by little rectangles. So, I cannot read any of the menus. Does anyone know how to fix this problem? I just installed phenix-1.3b-d7-intel-linux-2.6 on our Linux machine 2.6.19-1.2911.fc6 i686 During installation, the following warning is reported : ... > (pango-querymodules:17819): Pango-WARNING **: Engine reported invalid > script value 56 > (pango-querymodules:17819): Pango-WARNING **: Engine reported invalid > script value 63 > (pango-querymodules:17819): Pango-WARNING **: Engine reported invalid > script value 64 > updating fonts/local.conf file > running mkfontdir > rebuilding font cache > fc-cache: symbol lookup error: fc-cache: undefined symbol: > FcConfigNormalizeFontDir > > generating index.theme file ... And I also get the following message when executing phenix > Shell variable RSH_PATH not set > Error reading Pango modules file > > (python:26803): Pango-WARNING **: pango_shape called with bad font, > expect ugly output > (python:26803): Pango-WARNING **: pango_font_get_glyph_extents called > with null font argument, expect ugly output > (python:26803): Pango-WARNING **: pango_font_get_metrics called with > null font argument, expect ugly output > (python:26803): Pango-WARNING **: _pango_cairo_font_install called > with bad font, expect ugly output > Thank you for any help you can give. Mike Sawaya

2 1

Re: [phenixbb] phaser with certain spacegroups
by Tom Terwilliger 29 Sep '07

29 Sep '07

Hi Joe, Yes, you can run phaser with a selected subset of the possible spacegroups in the GUI. Here is how: 1. Start the AutoMR wizard as usual, and on the 2nd screen... A. say Yes to "Search all (selected) space groups with same point group" B. Under 'Choose variable to set' , select "all_plausible_sg_list" 2. Then hit CONTINUE and you will get a list of space groups. Edit out the ones you do not want with "Parameter group options" button. You're done. When you hit CONTINUE again the wizard will carry on with just the selected space groups. 3. If you want to make sure everything is ok, before you hit CONTINUE in step 2 after selecting the space groups you like, you can also select "Search Criteria" in NAVIGATE and then the 2nd screen will come up again with just the space groups you chose. All the best, Tom T At 12:31 PM 9/28/2007, Joe Batchelor wrote: >Hi, > >Can I run phaser through the phenix GUI using some, but not all, of >the possible spacegroups? > >Thanks, >Joe >_______________________________________________ >phenixbb mailing list >phenixbb(a)phenix-online.org >http://www.phenix-online.org/mailman/listinfo/phenixbb Thomas C. Terwilliger Mail Stop M888 Los Alamos National Laboratory Los Alamos, NM 87545 Tel: 505-667-0072 email: terwilliger(a)LANL.gov Fax: 505-665-3024 SOLVE web site: http://solve.lanl.gov PHENIX web site: http:www.phenix-online.org ISFI Integrated Center for Structure and Function Innovation web site: http://techcenter.mbi.ucla.edu TB Structural Genomics Consortium web site: http://www.doe-mbi.ucla.edu/TB

1 0

phaser with certain spacegroups
by Joe Batchelor 28 Sep '07

28 Sep '07

Hi, Can I run phaser through the phenix GUI using some, but not all, of the possible spacegroups? Thanks, Joe

1 0

Bulk solvent scaling problems
by seglynn 25 Sep '07

25 Sep '07

Dear all, I am using phenix.refine for the first time to refine a 4.5A structure solved by MR with individual sites (stretching things a bit, I know) and a grouped ADP per domain. Below are the R-factor per cycle stats: REMARK ------------------------------------------------------------------------ REMARK R-factors, x-ray target values and norm of gradient of x-ray target REMARK stage r-work r-free xray_target_w xray_target_t REMARK 0 : 0.6464 0.6186 7.101344e+00 7.091899e+00 REMARK 1_bss: 0.3955 0.4006 6.825652e+00 6.806242e+00 REMARK 1_xyz: 0.3200 0.3622 6.675328e+00 6.720706e+00 REMARK 1_adp: 0.3201 0.3622 6.674498e+00 6.719426e+00 REMARK 2_bss: 0.3539 0.3804 6.736883e+00 6.752128e+00 REMARK 2_xyz: 0.3067 0.3427 6.639056e+00 6.687071e+00 REMARK 2_adp: 0.3062 0.3423 6.638917e+00 6.687168e+00 REMARK 3_bss: 0.3357 0.3685 6.706475e+00 6.735398e+00 REMARK 3_xyz: 0.3082 0.3469 6.652536e+00 6.702364e+00 REMARK 3_adp: 0.3076 0.3468 6.652984e+00 6.703972e+00 REMARK 3_bss: 0.3286 0.3659 6.701854e+00 6.743421e+00 REMARK ------------------------------------------------------------------------ You can see that after the intial scaling, each cycle of bulk solvent scaling and anisotropy correction leads to an increase in R-factors of ~2%. Has anyone seen this behaviour before and maybe suggest a solution? Alternatively, is there a way I can turn off the final cycle of bulk solvent scaling before outputting the pdb and maps? Thanks in advance, Steve Glynn

2 1

Oxygen atoms in phenix.refine
by Daniele de Sanctis 25 Sep '07

25 Sep '07

Dear all, i'm experiencing a weird problem with phenix.refine. After a phenix.refine run with a pdb file that doesn't contain the atoms N, CA, C, and O all together (with sidechains atoms between C and O) the O atoms are displaced from their position. Is this a know problem? Is there anyone that have suggestions how to re-edit the pdb file accordingly instead of doing cut-past for too many atoms? thanks daniele -- Daniele de Sanctis, PhD Homo sum humani nil alienum a me puto ______________________________________________________________ phone ++ 351 21 4469 662 fax ++ 351 21 4433 664 e-mail de.sanctisd(a)gmail.com, sanctis(a)itqb.unl.pt Mailing address: ITQB, Av. República, Apartado 127 2781-901 Oeiras Portugal

2 1

phenix and ncs
by Jan Abendroth 23 Sep '07

23 Sep '07

Hi all, I could not quite find an answer in the on-line documentation: - How does phenix.refine use ncs restraints? Does it use xyz or torsion angle restraints? - Can one define the tightness of the ncs restraints? - Can one put different restraints on mainchain and sidechain atoms? Cheers Jan -- Jan Abendroth deCode Biostructures Seattle/Bainbridge Island, WA, USA work: JAbendroth(a)decode.is home: Jan.Abendroth(a)gmail.com

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elbow builder / phenix question
by Sudharsan Sridharan 20 Sep '07

20 Sep '07

Hi all, Is it ok to use the cif files generated by PRODRG server directly in phenix refine ? I fit a ligand molecule in density in Coot using this cif file. but after refinement in phenix using the same cif file the ligand coordinates does not look right. Then I created a new cif file using elbow.builder (with final geometry option) for the coordinates fit in Coot. But I see differences in the bond properties in the new cif file compared with the one from PRODRG server. e.g. please see below for parts of the cif generated in these two. could you please advice how to get the right cif file using the server or phenix and do the refinement. in a related question, is the command to use for building the cif in phenix phenix.elbow or elbow.builder. the former is given in http://www.phenix-online.org/new-site/documentation/elbow.htm but didn't work (i'm using 1.3 beta) and the latter does work (which is good !). Thanks, Sid. from prodrg: DRG OAB CAK deloc 1.250 0.020 DRG CAK OAD deloc 1.250 0.020 DRG CAK CAM single 1.530 0.025 DRG CAM CAA double 1.390 0.020 DRG CAM OAJ single 1.360 0.022 DRG OAJ CAO single 1.435 0.033 DRG CAO CAI single 1.390 0.020 DRG CAO CAP single 1.530 0.025 DRG CAI CAG double 1.390 0.020 DRG CAG CAH single 1.390 0.020 DRG CAH CAN double 1.390 0.020 DRG CAN CAL single 1.530 0.025 DRG CAN CAP single 1.530 0.025 DRG CAL OAE deloc 1.250 0.020 DRG CAL OAC deloc 1.250 0.020 DRG CAP OAF single 1.430 0.025 DRG OAF HAA single 1.000 0.027 DRG CAA 1HAA single 1.000 0.020 DRG CAA 2HAA single 1.000 0.020 DRG CAO 1HAO single 1.000 0.020 DRG CAI 1HAI single 1.000 0.020 DRG CAG 1HAG single 1.000 0.020 DRG CAH 1HAH single 1.000 0.020 DRG CAP 1HAP single 1.000 0.020 from elbow.builder: ISC OAB CAK double 1.23599 0.02 ISC CAK OAD single 1.23956 0.02 ISC CAK CAM single 1.51571 0.02 ISC CAM CAA single 1.38593 0.02 ISC CAM OAJ single 1.35985 0.02 ISC OAJ CAO double 1.45557 0.02 ISC CAO CAI aromatic 1.38350 0.02 ISC CAO CAP aromatic 1.53664 0.02 ISC CAI CAG aromatic 1.37763 0.02 ISC CAG CAH aromatic 1.37668 0.02 ISC CAH CAN aromatic 1.37587 0.02 ISC CAN CAL single 1.53109 0.02 ISC CAN CAP aromatic 1.52972 0.02 ISC CAL OAE double 1.22830 0.02 ISC CAL OAC single 1.23738 0.02 ISC CAP OAF double 1.41071 0.02 ISC 1HAD OAD single 1.08000 0.02 ISC 1HAM CAM single 1.08000 0.02 ISC 1HAA CAA single 1.08000 0.02 ISC 2HAA CAA single 1.08000 0.02 ISC 3HAA CAA single 1.08000 0.02 ISC 1HAH CAH single 1.08000 0.02 ISC 1HAC OAC single 1.08000 0.02

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wxu scale in phenix.refine
by Jan Abendroth 18 Sep '07

18 Sep '07

Hi all, in the final stages of refining a structure, I would like to optimize the restraint weights for geometry and B factors. It seems to work fine for geometry by defining " refinement.target_weights.wxc_scale=1.0". However, when the respective definition for B-factors does not seem to have an impact at all. I tried both: "refinement.target_weights.wxu_scale=2.0" in the parameter file or "wxu_scale=2.0" in the command line. The main reason why I try to fiddle around with the B-weights is that coot gives me a whole bunch of red bars in the Temperature factor variance analysis... I am using phenix 1.3d (downloaded past Sunday), mac-intel-osx, osx-10.4.10 Any ideas? Cheers Jan

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Re: [phenixbb] Problem in Autosol
by Eric Tee 16 Sep '07

16 Sep '07

Hi Tom, Many thanks for your reply. I was running phenix in my d_drive (a vfat partition) and got the error message. However, when I moved the mtz file to a directory under home directory (home/user/phenix-local), The program work without any problem. Let me explain how this work: I'm running phenix on fedora7 (a dual boot machine with Windows). I installed phenix under home/user/program/phenix (not /usr/local). I have a vfat partition (as d_drive) where I keep all my data and basically process everything there. I got the error message if I run phenix in the vfat partition but the program can be run successfully under the home directory /home/user/phenix-local). Following is what I got if I run phenix in the vfat partition (d_drive): WORKDIR: /mnt/d_drive/ccp4_data/SAD/phenix-localmachine Checking for KnownWizards: ['AutoSol', 'AutoBuild', 'ImportRawData'] application method: Null Getting inputs on first pass... SETTING UP INPUTS AutoSol Wizard Screen 1 of 4 AutoSol: Choose data files for dataset #1 A "dataset" is a group of data with a single set of heavy-atom sites You will be able to combine the results of all datasets later Note: Data files can be any format. If they are not all Scalepack premerged or all Scalepack unmerged then all will be converted to Scalepack premerged SUMMARY Input files dataset #1 Se_pk.mtz Creating new Data Storage /mnt/d_drive/ccp4_data/SAD/phenix-localmachine/PDS/AutoSol.1 sh: TEMP0/temporary.com: Permission denied Could be something related to permission problem but I have set permission to read/write/execute in vfat partition by adding the following line to /etc/fstab: /dev/sda6 /mnt/d_drive vfat users,uid=eric,gid=users,umask=0002,utf8=true 0 0 Any suggestion to enable running phenix in the vfat partition? Eric On 9/16/07, Tom Terwilliger <terwilliger(a)lanl.gov> wrote: > > Hi Eric, > > Can you possibly check to see that you have a recent version of phenix: > > phenix.version will do this. > > > Then if that is ok, I'm not sure what is causing the problem. This > message means that solve could not run with the data it got, but > usually an error message should come up earlier if there is a > problem. Have a look at LAST.LOG in your AutoSol directory and see > if it has any hints. Also look at AutoSol_run_1_.output and see the > end of this log file. > > If none of those work, if you can send me your input data file I can > see if there is a problem with it (all I would need is the first 100 > lines or so). > -Tom T > >

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Problem in Autosol
by Eric Tee 15 Sep '07

15 Sep '07

Hi All, I was trying to run SAD phasing with phenix GUI for the first time. After conversion of mtz to sca file, at the step of autosol_scale_and_analyze_mad, I got the following message: failed to carry out Autosol_scale_and_analyze_mad None of the solve versions worked I'm pretty sure I choose the right package. Should I do something to configure solve? Eric

1 0

elbow.builder to generate charges on individual atoms?
by Francis E Reyes 13 Sep '07

13 Sep '07

Ok, this is probably an unsupported feature(TM),but is there anyway to hack elbow.builder to output an electronic charge (presumably from the AM1 calculation) for each atom of a ligand? (by say substituting in for the Bfactor)) Thanks FR --------------------------------------------- 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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Position for PSI Knowledgebase development
by Paul Adams 12 Sep '07

12 Sep '07

======================================================================= Lawrence Berkeley National Laboratory Software Developer II ======================================================================= Software Developer II Job ID: 20930 Division: Physical Biosciences Date Opened: 8/7/2007 Summary This position will be part of the Computational Crystallography Initiative at Lawrence Berkeley Lab and will be responsible for developing a web site to disseminate information about the Technologies developed by the NIH Protein Structure Initiative (PSI). This program funds the majority of structural genomics efforts within the US and is responsible for the development of many new technologies that are useful to macromolecular crystallographers. This technology resource is part of the larger PSI Knowledge Base that will provide an information portal for the scientific community. Duties Essential: Under general direction of the Principal Investigator: Develop and maintain web site documenting PSI developed technologies. Interact with PSI researchers to collect information about new technologies. Create a relational database to store crystallographic data. Install and maintain SVN repositories for the PSI community. Marginal: Perform routine analysis of crystallographic data. Maintain web site computing hardware and software. Other duties as assigned. Qualifications Essential: Experience with writing and maintaining HTML web pages. Knowledge of standard programming methods, and Python in a UNIX environment. Strong analytical and organizational skills. Ability to handle multiple tasks in parallel. Excellent interpersonal skills for working in a diverse team environment, ability to interact effectively with other scientists, and to address their needs in an effective and timely manner. Marginal: B.S. Degree or higher in biophysics, computer science, chemistry, electrical engineering, physics or related field preferred or equivalent experience, with demonstrated programming experience. Experience maintaining computing hardware and software. Experience with analysis of crystallographic data. NOTE: This is a one year Term appointment with the possibility of renewal under the same terms and conditions, contingent upon continued funding and availability of work. Lawrence Berkeley National Laboratory is a world leader in science and engineering research, with 11 Nobel Prize recipients over the past 75 years, and 59 present members of the National Academy of Sciences. LBNL conducts unclassified research across a wide range of scientific disciplines and hosts four national user facilities. AA/ EEO employer committed to the development of a safe and diverse workforce. Learn more at http://www.lbl.gov. For more information about the CCI visit: http://cci.lbl.gov/ To apply: visit http://cjo.lbl.gov/ and search for the job number 20930. Please see http://cjo.lbl.gov/app_instr.html for details of how to apply. -- Paul Adams Senior Scientist, Physical Biosciences Division, Lawrence Berkeley Lab Adjunct Professor, Department of Bioengineering, U.C. Berkeley Head, Berkeley Center for Structural Biology Deputy Principal Investigator, Berkeley Structural Genomics Center Building 64, Room 248 Tel: 510-486-4225, Fax: 510-486-5909 http://cci.lbl.gov/paul Lawrence Berkeley Laboratory 1 Cyclotron Road BLDG 64R0121 Berkeley, CA 94720, USA. --

1 0

pseudo-merohedral twinning in P212121
by Schneider Sabine 12 Sep '07

12 Sep '07

Hi everyone, I have a data set to 2.8A, with most likely 2 molecules in the asu and a molecular replacement model with 40% sequence identity. (Cell 71.3 71.3 227.9 90 90 90) Initially the data appeared to be either P4322 or P43212 (Rsym = 7.4%; Cell 71.3 71.3 227.9 90 90 90), but the molecular replacement solutions had major clashes with the symmetry related molecules and a lower LLG for the solution of the second molecule. No twinning was detected by Xtriage. Processing the data in P212121 (Rsym 5.6%, cell 71.3 71.4 228.2 90 90 90) gave me a better molecular replacement solution (LLG 121/373), but I had 5 clashes with the second molecule in the asu. (I tested all alternative spacegroups) I also have a MAD dataset (very low quality!) and I combined the phases with the one obtained from molecular replacement in Sharp. After NCS averaging the maps had improved (still not great). I tried to improve things in the model and run Phaser again and the solution had better statistics (LLG 338/1223) and the clashes were reduced to 2. Xtriage detected pseudo-merohedral twinning with a twin fraction of 43% with twin operator -k, -h, -l. So I tried refining the model with phenix telling it the twinning operator and fraction, but R/Rfree are stuck around 45%. I also tried simulated annealing but that gave even higher R/Rfree. Is there anything I can do, or is it a hopeless case? Thanks for your help in advance! Sabine This message has been checked for viruses but the contents of an attachment may still contain software viruses, which could damage your computer system: you are advised to perform your own checks. Email communications with the University of Nottingham may be monitored as permitted by UK legislation.

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phenix.refine error
by Jianghai Zhu 12 Sep '07

12 Sep '07

Hi, I was trying the twinning refinement by phenix.refine and I got the following error messages during TLS refinement. Traceback (most recent call last): File "/nfs/home/jzhu/cci_apps_sources/phenix/phenix/command_line/ refine.py", line 5, in <module> command_line.run(command_name="phenix.refine", args=sys.argv[1:]) File "/nfs/home/jzhu/cci_apps_sources/phenix/phenix/refinement/ command_line.py", line 81, in run call_back_after_monitor_collect=call_back_after_monitor_collect) File "/nfs/home/jzhu/cci_apps_sources/phenix/phenix/refinement/ driver.py", line 1244, in run log = log) File "/nfs/home/jzhu/cci_apps_sources/phenix/phenix/refinement/ strategies.py", line 866, in refinement_machine h_params = h_params) File "/nfs/home/jzhu/cci_apps_sources/mmtbx/mmtbx/refinement/ adp_refinement.py", line 175, in __init__ macro_cycle = macro_cycle) File "/nfs/home/jzhu/cci_apps_sources/mmtbx/mmtbx/tls/tools.py", line 600, in __init__ fmodel.info().show_targets(text = prefix+" start model", out = out) AttributeError: 'info' object has no attribute 'show_targets' Could somebody help me? Thanks. Jianghai PS. the version is 2007_08_18_1856. +++++++++++++++++++++++++++++++ Jianghai Zhu, Ph.D CBR Institute for Biomedical Research Department of Pathology Harvard Medical School 200 Longwood Ave., Boston, MA 02115 Ph: 617-278-3211 Fx: 618-278-3232 +++++++++++++++++++++++++++++++

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What does mmtbx.twin_map_utils output?
by Francis E Reyes 11 Sep '07

11 Sep '07

Specifically I'm asking about the obs_and_calc.mtz file it produces. Thanks FR --------------------------------------------- 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

2 3

So I think I have a twinning problem... ?
by Francis E Reyes 10 Sep '07

10 Sep '07

Hi all The short of the long is that phenix.xtriage on a C2 data set shows twinning with 3 twinning operators (-h,-k-l -k-h-l and k,h,-l). Pushing it through twin_utils, the soution k,h,-l gives an r/rfree of 0.30 and 0.3014 when the twin fraction is 0.352 . The question is where to go from here? I try to phenix.refine the same model in phenix.xtriage (except the mtz file is from the latest round of refinement of that model) and the R/Rfree on macro cycle =2 is 30 and 34 . Unfortunately, it doesn't seem to finish the refinement, I get a seg fault. In the def file for the refinement I set twinning = True and twin_law = k,h,-l . I tried to subject the same model and the .ref file to an autobuild passing in a .eff file for refinement specifying the twin_law, and again I get a segfault / crash when refining the input model. Please advise! --------------------------------------------- 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

2 1

Twinning in phenix.autobuild?
by Francis E Reyes 10 Sep '07

10 Sep '07

Hello all So I discovered from xtriage that my crystal is twinned. I have a pretty decent model that xtriage says has an r/rfree of 30/30 to a resolution of 2.6. I wanted to try a phenix.autobuild at 2.8A. I couldn't find a parameter flag for autobuild that turns on twinning. I already autobuilt this model once, and the xtriage log did find that the crystal was twinned, but twinning in refinement of the model during rebuilding wasn't turned on. Is there a way to tell autobuild to rebuild using twinning? Thanks FR --------------------------------------------- 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

3 3

crash during refinement with twinned data
by Scott White 10 Sep '07

10 Sep '07

Dear PhenixBB, I'm trying to refine a structure against potentially twinned data. I got the twin law from xtriage. phenix.refine starts, and at some point crashes with the messages below. Refinement proceeds to the end if I don't include twinning. Any suggestions? Thanks, Scott Traceback (most recent call last): File "/software/phenix-1.3b/phenix/phenix/command_line/refine.py", line 5, in <module> command_line.run(command_name="phenix.refine", args=sys.argv[1:]) File "/software/phenix-1.3b/phenix/phenix/refinement/command_line.py", line 81, in run call_back_after_monitor_collect=call_back_after_monitor_collect) File "/software/phenix-1.3b/phenix/phenix/refinement/driver.py", line 1325, in run log = log) File "/software/phenix-1.3b/phenix/phenix/refinement/strategies.py", line 559, in refinement_machine log = log) File "/software/phenix-1.3b/mmtbx/mmtbx/refinement/rigid_body.py", line 347, in __init__ fmodel_copy = fmodel.resolution_filter(d_min = res) File "/software/phenix-1.3b/mmtbx/mmtbx/twinning/twin_f_model.py", line 1042, in resolution_filter sf_and_grads_accuracy_params = dc.sfg_params File "/software/phenix-1.3b/mmtbx/mmtbx/twinning/twin_f_model.py", line 890, in __init__ u_part=self.scaling_parameters.u_part ) RuntimeError: cctbx Internal Error: /net/anaconda/scratch1/phenix/phenix-1.3b/cctbx/include/cctbx/xray/f_model.h(91): CCTBX_ASSERT((f_mask.size() == 0) || (hkl.size() == f_mask.size())) failure. -- _______________________________________ Dr Scott A. White Protein Crystallography Group School of Biosciences University of Birmingham B15 2TT E: s.a.white(a)bham.ac.uk T: +44-(0)121-414-7534 F: +44-(0)121-414-5925 W: http://www.bip.bham.ac.uk/cryst ______________________________________

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Re: [phenixbb] Unknown atoms revisitied
by Ralf W. Grosse-Kunstleve 07 Sep '07

07 Sep '07

> Does the atom type have to be a known element or can it something like > element X as seen in some pdb files? > > An example from 1aqn: > HETATM 1951 UNK UNX 277 -4.541 50.540 38.754 0.25 13.93 X > HETATM 1952 UNK UNX 278 -4.443 49.701 37.169 1.00 15.64 X Pavel is correct, but I'll add a some more details. If you want to use these atoms in refinement, you have to decide what scattering type to use. That has to be one of the symbols published in the International Tables for Crystallography, Volume C (see cctbx/eltbx/xray_scattering/it1992.cpp under $PHENIX or cci_app_sources). Regarding the .cif file: data_comp_SIN loop_ _chem_comp_atom.comp_id _chem_comp_atom.atom_id _chem_comp_atom.type_symbol _chem_comp_atom.type_energy _chem_comp_atom.partial_charge SIN N N N 0.000 | | | | | this must be a valid "energy type" (see below) | this must be a valid scattering type symbol (Int. Tab.) this can be anything you want mon_lib/ener_lib.cif defines energy types (phenix.where_mon_lib_list_cif shows the path to mon_lib). You can define other energy types in additional .cif files you give to phenix.refine, using the same syntax as in the central ener_lib.cif. Regarding the .pdb file: HETATM 1952 UNK UNX 278 -4.443 49.701 37.169 1.00 15.64 X | | | | this must match the data_comp_UNX | | this must match _chem_comp_atom.type_symbol this must match _chem_comp_atom.atom_id You cannot use X in columns 77-78 because it must match _chem_comp_atom.type_symbol, and that in turn must be a valid scattering type symbol. However, you can leave the column blank. I think I'll change phenix.refine to treat the X like a blank, then you don't have to remove it. But in the current release you have no choice. Ralf

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Re: [phenixbb] Unknown atoms revisitied
by Ralf W. Grosse-Kunstleve 06 Sep '07

06 Sep '07

Hi Jeff, > I was wondering if there were any way to have a single unknown atom > recognized by phenix for refinement. Make up any residue name you like, e.g. SIN (for single N). Create a .cif file like this: data_comp_SIN loop_ _chem_comp_atom.comp_id _chem_comp_atom.atom_id _chem_comp_atom.type_symbol _chem_comp_atom.type_energy _chem_comp_atom.partial_charge SIN N N N 0.000 In your PDB file add: ATOM 68 N SIN 15 20.000 20.000 20.000 1.00 20.00 N Add the name of the .cif file to the phenix.refine command line. You can have more than one data_comp_ in the same cif file, if you want to use different element types. Ralf

1 0

Unknown atoms in refinement
by Jeff Habel 06 Sep '07

06 Sep '07

What's the best way of dealing with unknown atoms (UNK) in phenix.refine? I have a long disordered loop that runs basically the length of the protein on the back side and there is a single "amino acid" in the middle that I'm trying to model as UNK. I can run a round of refmac and auto generate a lib file with my ligand and the unk atoms but phenix.refine balks at that with respect to the Van der Waals radii. Thanks for the help, -Jeff

4 5

wxu_scale during TLS + INDIVIDUAL_ADP refinement
by Jose M de Pereda 06 Sep '07

06 Sep '07

Dear colleagues, I am refining a structure with phenix.refine (cci_apps 2007_08_18_1856). The strategy includes refinement of tls, individual_adp, and individual_sites (during the same run.) In order to test different restraints for ADP´s refinement, I have changed the value of the wxu_scale from the default. Yet, the value of the wxu_scale parameter is always automatically reset to the same value as indicated in the log file under the section "Automatic adjustment due to TLS refinement". That is, phenix.refine uses in all cases the same wxu_scale independently of the value I set in the definitions file. Of course, when TLS refinement is not done, the wxu_scale value remains as specified. I would appreciate if someone could indicate me how to modify the ADPs restraints when doing TLS refinement. Cheers Jose -- -------------------------------------------------- Jose M de Pereda, PhD Centro de Investigación del Cáncer Spanish National Research Council - U. Salamanca Campus Unamuno s/n E-37007 Salamanca, Spain Phone: +34-923-294819 Fax: +34-923-294795 http://xtal.cicancer.org/ -------------------------------------------------

2 1

statistics for highest shell in phenix.refine
by michael hothorn 05 Sep '07

05 Sep '07

Dear all, For the crystallographic table in my manuscript, can I define a highest shell in phenix.refine and have it output the refinement statistics for this range? If not, how can I calculate the highest shell statistics using the same parameters as used for the overall refinment? Thanks Michael

2 1

Re: [phenixbb] selective nonbonded restraint removal
by Cathy Lawson 05 Sep '07

05 Sep '07

Thanks to all who replied. And thank you Ralf for your suggestion (quoted below), this worked very nicely! Somehow I missed this possibility in the online documentation. To reply to Pavel's question regarding how I figured out that tris is present at 1/2 occupancy: (1) density was first modelled with waters but they were too close together, and there was a fairly clear tetrahedral shape. (2) phosphate didn't refine well -- lead to huge negative difference peak at the P atom. (3) only other tetrahedral shape molecule in the soup was tris (TAM), and after refining just the tetrahedral core it was possible to see where the three arms extended. (4) b-factors for the tris were high relative surrounding protein atoms, and extraneous density suggested two alternate conformations for the nearby arg side-chain, one of which is too close to realistically exist next to the tris ligand. the other clue was that trial occupancy refinement of all atoms put most tris atoms in the 0.4-0.6 occupancy range. (5) tris with 0.5 occupancy, arg with two alt confs, plus a few waters at 0.5 occupancy is so far the best model with no significant different densities for this region. (6) the modelling will need to be confirmed with an SA omit ... > Hi Cathy, > > > The density suggests that when tris is not there, > > a side chain moves very close to that position > > You could model this with alternative conformations. If you assign > "altloc" A and B to two conformers of your protein, and just, say, B > to your TAM, then the ligand would only "see" your B protein. If you > don't define the B conformer (no atoms) then TAM wouldn't see that > part of the protein at all. > Actually, this approach seems better to me than working with > atom selections. > > Ralf

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Re: [phenixbb] selective nonbonded restraint removal
by Cathy Lawson 05 Sep '07

05 Sep '07

Hi Ralf, That is disappointing. Lovely maps produced after a few phenix.refine runs for a 1.6 A structure revealed an unexpected tris ligand (TAM) with occupancy ~0.5. The density suggests that when tris is not there, a side chain moves very close to that position, thus my question. In other regards phenix seems a great step forward in automating refinement, and I look forward to new developments. best wishes, Cathy > Hi Cathy, > > > Is it possible to turn off nonbonded restraints for particular > > residues/monomers, or for atoms with occupancy less than 1.0? > > Nope, sorry. It is on the (long) to-do list. > BTW: each time someone asks the priority goes up. > > Ralf

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selective nonbonded restraint removal
by Cathy Lawson 04 Sep '07

04 Sep '07

Hi Phenix bber's, I have been trying out phenix.refine and like it very much so far. Is it possible to turn off nonbonded restraints for particular residues/monomers, or for atoms with occupancy less than 1.0? Thanks, Cathy Lawson /////////////////////////////////////////////////////// http://rutchem.rutgers.edu/~lawson

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