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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.)

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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 24 Jul '11

24 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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Protein expression, purification and crystallization
by Hena Dutta 21 Jul '11

21 Jul '11

Dear Members of CCP4BB and PHENIXBB, Can you suggest a reliable website where I can get basic and advanced information on protein expression, purification and crystallization. I like to read on the monitor. Thanking you in advance... Hena

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phenix.phaser PATH problem
by G P 21 Jul '11

21 Jul '11

Dear all, It's long story: At beginning, I have phenix installed. I do not have CCP4 installed. Then I run "phenix.phaser params.eff" to call phenix run phaser from script params.eff. It works well. Then, I installed CCP4 with its own phaser inside. Then I run again "phenix.phaser params.eff". The computer start to import files (should be some libraries and supporting files, not input data) from CCP4 installation directory. It seems so strange for me. And because some of the .so files in CCP4 directory are for 32bit, phenix.phaser gave me error message: wrong ELF class: ELFCLASS32 and refused to keep running. I guess I could solve this problem by copying the same .so file in phenix directory into CCP4's directory. What I really want to know is why this happen. Is that the installation of CCP4 changed some kinds of PATH variables for phenix? How could I fix by giving a right path again? I would appreciate to any help. Thanks a lot guys! Best regards, GP

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phenix.phaser multiple models
by G Y 21 Jul '11

21 Jul '11

Dear all, I want to give several input pdb (searching model) at same time and let phaser run MR separately on each of them. I found I can do this by first "Add ensembles" at Ensemble tab and then "Add search" at Search procedure tab then link the correct ensemble ID. However, there is just one output result for the best solution. Is there anyway to get all solutions in separate .mtz and .pdb files for different searching models? Many thanks! regards, G

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problem in rosetta rebuilding
by intekhab alam 20 Jul '11

20 Jul '11

Hi i tried to run rosetta on a unix machine (ubuntu 9.04) for my data. Upto MR step everything goes fine , but during the rebuilding step after 20 cycles the computer shuts down. i have attached the log file for the autobuilding run of rosetta. i am using phenix 1.7.1-743 version. i will be grateful if some one helps me out -- INTEKHAB ALAM LABORATORY OF STRUCTURAL BIOINFORMATICS KOREA UNIVERSITY, SEOUL

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