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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

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

26 Jul '11

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

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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

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mr_rosetta with fixed solutions for other chains
by Bard, Joel 26 Jul '11

26 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

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cif file for internal bond with one of two alternative conformations
by Daqi Tu 26 Jul '11

26 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.)

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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

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Alternate conformer and HOH clashes
by Yuri 25 Jul '11

25 Jul '11

Thanks guys... What about waters, do they follow the same ALTLOC rules? I have a high res data 1A and I see lots of things... Ill probably bother you again with some questions as I keep refining. Best, Yuri -- Yuri Pompeu

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Alternate conformer and HOH clashes
by Yuri 24 Jul '11

24 Jul '11

Dear All, I am having trouble refining multiple conformers that would clash into a neighbouring side chain that also has an alternate conformer. An attempt to clarify: Lets say a Tyr residue has conformation A1, but also moves into a position B1. In postition B, its side chain would clash into a neighbour Phe A2. However this Phe has another conformation B2. Bottom line, B1 and B2 would not clash, neither would A1 and A2. Any other combo (A1 B2, etc...) would clash. When I model it all in I see problems... I encounter the same situation with partially occupied HOHs. Whats the best way to deal with this Thank you -- Yuri Pompeu

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Latest Build Error
by Yuri 22 Jul '11

22 Jul '11

I installed the latest dev-826 version and the GUI does not open phenix_refine. I get a fatal error message. thank you -- Yuri Pompeu

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restraints for D3O+ give problems to run in phenix.refine
by Maxime Cuypers 22 Jul '11

22 Jul '11

hello, apologies if this problem has already been reported, i browsed for a while and i am running out of ideas to solve my problem. i have a neutron structure i was refining fine with phenix.refine untill i had to add a D3O water. description: running phenix.elbow or phenix.refine with .cif file for D3O i am getting the following error: ... Residues with excluded nonbonded symmetry interactions: 1 residue: pdb=" O D3O W 1 " occ=0.53 ... (2 atoms not shown) pdb=" D3 D3O W 1 " occ=0.53 Number of atoms with unknown nonbonded energy type symbols: 3 "HETATM 2 D1 D3O W 1 .*. D " "HETATM 3 D2 D3O W 1 .*. D " "HETATM 4 D3 D3O W 1 .*. D " Time building chain proxies: 0.01, per 1000 atoms: 2.50 Sorry: Fatal problems interpreting PDB file: Number of atoms with unknown nonbonded energy type symbols: 3 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. Also note that phenix.ready_set and phenix.elbow are available for creating restraint definitions (CIF files). ******************* i then modified the .param file implementing the apply_cif_modification and apply_cif_link parameters: refinement { main { number_of_macro_cycles = 10 ordered_solvent= false scattering_table= neutron } hydrogens { refine= individual } pdb_interpretation.apply_cif_modification { data_mod = D3O residue_selection = resname D3O } pdb_interpretation.apply_cif_link { data_link = D3O residue_selection_1 = chain W and resname D3O } } ... ************************** the .cif file i have was created with phenix.ready_set: ( i added first line after it failed without) data_mod_D3O # 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 D3O D3O Unknown ligand 4 1 . # data_comp_D3O # 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 _chem_comp_atom.x _chem_comp_atom.y _chem_comp_atom.z D3O O O O -0.475 -12.5180 -14.4044 -43.0985 D3O H1 D D -0.294 -11.4013 -13.8002 -42.6392 D3O H2 D D -0.294 -13.3333 -13.3284 -43.0933 D3O H3 D D 0.063 -12.3324 -14.5311 -44.0190 # 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 D3O O H1 single 1.350 0.040 D3O O H2 single 1.350 0.040 D3O O H3 single 0.947 0.010 # 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 D3O H2 O H1 98.14 3.000 D3O H3 O H1 103.20 1.194 D3O H3 O H2 103.22 1.252 ********************************** whatever i do i systematically get the same error: Monomer Library directory: "/usr/local/phenix-1.7.1-743/chem_data/mon_lib" Total number of atoms: 1165 Number of models: 1 apply_cif_modification: data_mod: D3O Sorry: Missing CIF modification: data_mod_D3O Please check for spelling errors or specify the file name with the modification as an additional argument. ******************************** the command i enter is: phenix.refine xxxx.pdb xxxx.mtz D3O.ligands.cif high_res_xxxx-neutron-long-D3O.params \ refinement.input.xray_data.labels='IMEAN,SIGIMEAN' i looked in the online phenix.refine manual but it is not mentionning what to do in such error case. where should i put "data_mod_D3O" in the parameter file? is it the real source of the error? Could someone help me figuring out a solution to get the restraints to work for D3O(+), please? Maxime

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