- phenixbb - phenix-online.org

Third issue of Computational Crystallography Newsletter
by Nigel Moriarty 28 Jul '11

28 Jul '11

Dear Colleagues, I am pleased to announce the publication of the third issue of the Computational Crystallography Newsletter: http://www.phenix-online.org/newsletter/ A listing of the articles and short communications is given below. Please note that the newsletter accepts articles of a general nature of interest to all crystallographers. Please send any articles to me at NWMoriarty(a)lbl.gov noting that there is a Word Template on the website to streamline production. Articles -------- Improved target weight optimization in phenix.refine Mite-y lysozyme crystal and structure Short communications -------------------- A lightweight, versatile framework for visualizing reciprocal-space data An extremely fast spotfinder for real-time beamline applications Hints for running phenix.mr_rosetta Cheers Nigel -- Nigel W. Moriarty Building 64R0246B, Physical Biosciences Division Lawrence Berkeley National Laboratory Berkeley, CA 94720-8235 Phone : 510-486-5709 Email : NWMoriarty(a)LBL.gov Fax : 510-486-5909 Web : CCI.LBL.gov

1 0

C=O-D(+) and COOD restraints for phenix.refine
by Maxime Cuypers 28 Jul '11

28 Jul '11

Hello, Apologies if this problem has been asked previously, but i can t seem to find a solution online. I have added deuterium atoms in an exotic part of amide group (main chain) R2-C=O-D (+) bond and on a side chain Glu R-COOD to my pdb. i need to get a .cif that would account for it and work with phenix.refine. However, ready_set does not create a .cif file for it as it does not find unrestrained atoms. "No unknown residues" i have formatted the pdb the following way, adding DX for example (see ***): ATOM 778 N GLU A 51 8.057 40.510 -2.596 1.00 9.23 N ATOM 779 CA GLU A 51 8.846 41.709 -2.789 1.00 10.29 C ATOM 780 CB GLU A 51 8.151 42.937 -2.157 1.00 10.64 C ATOM 781 CG GLU A 51 6.672 43.097 -2.610 1.00 14.50 C ATOM 782 CD GLU A 51 6.543 43.007 -4.130 1.00 12.87 C ATOM 783 OE2 GLU A 51 6.056 42.014 -4.689 1.00 12.79 O ATOM 784 OE1 GLU A 51 6.987 43.967 -4.788 1.00 14.44 O ATOM 785 C GLU A 51 10.293 41.604 -2.286 1.00 8.42 C ATOM 786 O GLU A 51 10.961 42.627 -2.213 1.00 11.96 O ATOM 787 D GLU A 51 7.625 40.435 -1.776 1.00 10.15 D ATOM 788 DA GLU A 51 8.957 41.874 -3.812 1.00 12.62 D ATOM 789 DB2 GLU A 51 8.172 42.833 -1.173 1.00 11.93 D ATOM 790 DB3 GLU A 51 8.654 43.758 -2.380 1.00 13.79 D ATOM 791 DG2 GLU A 51 6.159 42.376 -2.149 1.00 11.66 D ATOM 792 DG3 GLU A 51 6.340 43.998 -2.326 1.00 14.27 D ***ATOM 793 DE1 GLU A 51 8.271 44.322 -5.268 1.00 30.00 D ATOM 850 N LEU A 56 20.084 37.831 -2.359 1.00 10.58 N ATOM 851 CA LEU A 56 21.370 38.483 -2.643 1.00 11.42 C ATOM 852 CB LEU A 56 21.801 39.360 -1.449 1.00 12.58 C ATOM 853 CG LEU A 56 20.783 40.461 -1.081 1.00 14.37 C ATOM 854 CD1 LEU A 56 21.278 41.264 0.152 1.00 16.71 C ATOM 855 CD2 LEU A 56 20.512 41.416 -2.257 1.00 17.46 C ATOM 856 C LEU A 56 22.415 37.441 -2.957 1.00 14.27 C ATOM 857 O LEU A 56 23.025 36.818 -2.093 1.00 30.34 O ATOM 858 D LEU A 56 19.954 37.597 -1.492 1.00 11.35 D ATOM 859 DA LEU A 56 21.249 39.065 -3.470 1.00 11.59 D ATOM 860 DB2 LEU A 56 21.898 38.760 -0.652 1.00 14.27 D ATOM 861 DB3 LEU A 56 22.681 39.834 -1.676 1.00 14.15 D ATOM 862 DG LEU A 56 19.925 39.988 -0.873 1.00 15.72 D ATOM 863 DD11 LEU A 56 20.622 41.969 0.365 1.00 17.87 D ATOM 864 DD12 LEU A 56 21.385 40.668 0.910 1.00 17.46 D ATOM 865 DD13 LEU A 56 22.131 41.691 -0.060 1.00 18.41 D ATOM 866 DD21 LEU A 56 19.968 42.175 -1.959 1.00 18.01 D ATOM 867 DD22 LEU A 56 21.384 41.721 -2.564 1.00 16.67 D ATOM 868 DD23 LEU A 56 20.043 40.956 -2.972 1.00 18.06 D ***ATOM 869 DX LEU A 56 22.482 36.144 -2.004 0.20 30.00 D I suspect i need to find a correct name for the D atoms, but i tried several already unsuccessfully. phenix.refine complains about 2 unrestrained atoms, the 2 D. Does someone know if there is a way to solve this issue or a workaround, please? thanks, Maxime

2 1

running geometry regularization on side chains only
by Francois Berenger 27 Jul '11

27 Jul '11

Hello, Is it possible to do phenix.pdbtools model.pdb --geometry_regularization but only allow sidechains to be corrected during the process? Thanks a lot, Francois.

3 4

Syntax Question
by Yuri 26 Jul '11

26 Jul '11

What is the syntax for refining occupancies of all the objects with ALTLOC assignments? thnkyou -- Yuri Pompeu

2 1

phenix.phaser params.eff output directory
by G Y 26 Jul '11

26 Jul '11

Dear all, I am writing a script for phenix.phaser. The keyword "output_dir" seems not work. In params.eff file I give it a line like: solution = None output_dir = /home/.../somedir/ keywords { general { root = "PHASER" title = "[no title set]" verbose = None debug = None mute = None xyzout = ON hklout = ON jobs = 2 } But I can not generate output file in the specified directory(somedir in the above case). The output files are always put in current working directory. Did I choose a wrong keyword to do this? What would be the correct way? Any answer would be appreciate greatly. Many thanks. regards, GP

2 3

Wrong e-mail, sorry
by Yuri 26 Jul '11

26 Jul '11

Please disregard the cif message... -- Yuri Pompeu

1 0

roche.cif
by Yuri 26 Jul '11

26 Jul '11

data_comp_list # loop_ _chem_comp.id _chem_comp.three_letter_code _chem_comp.name _chem_comp.group _chem_comp.number_atoms_all _chem_comp.number_atoms_nh _chem_comp.desc_level DRG DRG 'DRG ' non-polymer 16 8 . # # --------------- # data_comp_DRG # 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 DRG CAB C CH3 0.094 DRG HAC H HCH3 0.014 DRG HAD H HCH3 0.013 DRG HAE H HCH3 0.013 DRG OAF O O2 -0.092 DRG CAH C C 0.233 DRG OAC O O -0.406 DRG CAG C C 0.004 DRG CAA C C2 0.033 DRG HAB H HC2 0.013 DRG HAA H HC2 0.013 DRG CAE C CH2 0.096 DRG HAF H HCH2 0.013 DRG HAG H HCH2 0.013 DRG OAD O OH1 -0.098 DRG HAH H HOH1 0.044 loop_ _chem_comp_tree.comp_id _chem_comp_tree.atom_id _chem_comp_tree.atom_back _chem_comp_tree.atom_forward _chem_comp_tree.connect_type DRG CAB n/a OAF START DRG HAC CAB . . DRG HAD CAB . . DRG HAE CAB . . DRG OAF CAB CAH . DRG CAH OAF CAG . DRG OAC CAH . . DRG CAG CAH CAE . DRG CAA CAG HAA . DRG HAB CAA . . DRG HAA CAA . . DRG CAE CAG OAD . DRG HAF CAE . . DRG HAG CAE . . DRG OAD CAE HAH . DRG HAH OAD . END loop_ _chem_comp_bond.comp_id _chem_comp_bond.atom_id_1 _chem_comp_bond.atom_id_2 _chem_comp_bond.type _chem_comp_bond.value_dist _chem_comp_bond.value_dist_esd DRG CAB HAC single 1.090 0.029 DRG CAB HAD single 1.090 0.029 DRG CAB HAE single 1.090 0.029 DRG OAF CAB single 1.430 0.025 DRG CAH OAF single 1.360 0.022 DRG CAH OAC double 1.230 0.017 DRG CAH CAG single 1.530 0.025 DRG CAG CAA double 1.530 0.025 DRG CAG CAE single 1.530 0.025 DRG CAA HAB single 1.090 0.029 DRG CAA HAA single 1.090 0.029 DRG CAE HAF single 1.090 0.029 DRG CAE HAG single 1.090 0.029 DRG CAE OAD single 1.430 0.025 DRG OAD HAH single 1.000 0.027 loop_ _chem_comp_angle.comp_id _chem_comp_angle.atom_id_1 _chem_comp_angle.atom_id_2 _chem_comp_angle.atom_id_3 _chem_comp_angle.value_angle _chem_comp_angle.value_angle_esd DRG HAC CAB HAD 109.500 3.333 DRG HAC CAB HAE 109.500 3.333 DRG HAC CAB OAF 109.500 3.333 DRG HAD CAB HAE 109.500 3.333 DRG HAD CAB OAF 109.500 3.333 DRG HAE CAB OAF 109.500 3.333 DRG CAB OAF CAH 109.500 3.717 DRG OAF CAH OAC 124.000 2.502 DRG OAF CAH CAG 115.000 2.505 DRG OAC CAH CAG 121.000 2.494 DRG CAH CAG CAA 115.000 2.505 DRG CAH CAG CAE 115.000 2.505 DRG CAA CAG CAE 115.000 2.505 DRG CAG CAA HAB 115.000 2.505 DRG CAG CAA HAA 115.000 2.505 DRG HAB CAA HAA 120.000 2.989 DRG CAG CAE HAF 109.500 3.333 DRG CAG CAE HAG 109.500 3.333 DRG CAG CAE OAD 109.500 2.717 DRG HAF CAE HAG 109.500 3.333 DRG HAF CAE OAD 109.500 3.333 DRG HAG CAE OAD 109.500 3.333 DRG CAE OAD HAH 109.500 3.139 loop_ _chem_comp_tor.comp_id _chem_comp_tor.id _chem_comp_tor.atom_id_1 _chem_comp_tor.atom_id_2 _chem_comp_tor.atom_id_3 _chem_comp_tor.atom_id_4 _chem_comp_tor.value_angle _chem_comp_tor.value_angle_esd _chem_comp_tor.period DRG var_001 HAC CAB OAF CAH 60.000 4.440 3 DRG var_002 CAG CAH OAF CAB 60.000 4.440 3 DRG CONST_001 CAE CAG CAH OAF 180.000 0.714 2 DRG CONST_002 HAA CAA CAG CAH 180.000 0.714 2 DRG var_003 OAD CAE CAG CAH 30.000 16.736 6 DRG var_004 CAG CAE OAD HAH 60.000 13.289 3 loop_ _chem_comp_chir.comp_id _chem_comp_chir.id _chem_comp_chir.atom_id_centre _chem_comp_chir.atom_id_1 _chem_comp_chir.atom_id_2 _chem_comp_chir.atom_id_3 _chem_comp_chir.volume_sign DRG chir_001 CAB HAC HAE HAD positiv DRG chir_002 CAE CAG HAG HAF positiv loop_ _chem_comp_plane_atom.comp_id _chem_comp_plane_atom.plane_id _chem_comp_plane_atom.atom_id _chem_comp_plane_atom.dist_esd DRG plan-01 OAF 0.030 DRG plan-01 CAH 0.030 DRG plan-01 OAC 0.030 DRG plan-01 CAG 0.030 DRG plan-01 CAA 0.030 DRG plan-01 HAB 0.030 DRG plan-01 HAA 0.030 DRG plan-01 CAE 0.030 # # --------------- # -- Yuri Pompeu

1 0

mr_rosetta with fixed solutions for other chains
by Bard, Joel 25 Jul '11

25 Jul '11

Hi- We have data for a crystal where two of three components have high homology search models and can be found with straightforward phaser runs but the third component has much weaker homology to anything in the pdb. Is there a way to provide the solution for the first two components and let mr_rosetta work on the third? Thanks, Joel

2 1

cif file for internal bond with one of two alternative conformations
by Daqi Tu 25 Jul '11

25 Jul '11

Hi, I have a structure of drug bound to a protein. The drug has two alternative conformations, in which one of them has an internal bond making it a cyclic compound. How do I refine a structure like this? What modification should I do to its cif file, which I generated using elbow without the internal bond. Thank you. Daqi Tu (sorry if I have double posted.)

2 1

phenix.phaser params.eff labin problem
by G P 25 Jul '11

25 Jul '11

Dear all, I am now writing a script for phenix.phaser. In the input file params.eff there is a keyword labin which corresponds to the labels inside input mtz files. The important columns in my ccp4 mtz file are FP, SIGFP. I edit the line of labin as: labin F=FP SIGF=SIGFP when running the script, it returns me: Syntax error: expected "=", found "F" (file "params.eff", line 9) So, I changed it like: labin=FP SIGFP when running, it gave me the message: Sorry: Couldn't find array FP SIGP in file I also tried: labin="FP" or labin = "FP SIGFP" or labin="labin F=FP" and so on. With nothing it can find the right columns. My mtz file should be not problem, I checked with mtzdmp, the columns FP and SIGFP were there and with phenix GUI this file works well. Would someone know exactly how to edit this line in params.eff? Many thanks! GP

3 7