- phenixbb - phenix-online.org

Switching off symmetry related van der waals in phenix.refine
by Chandrika Deshpande 01 May '09

01 May '09

Hello everyone, I am using Phenix.refine to refine one of my protein structures. My protein crystallised in the spacegroup P6522 with one protein molecule in the asymmetric unit. I have a PEG molecule from the crystallization condition which crosses a two-fold crystallographic symmetry axis. PEG is symmetric hence this does not violate the crystal symmetry. However, this situation causes a problem which I need to solve : How can I refine this structure to include the PEG molecule? Is there a way to remove van der Waals repulsion between one half occupancy PEG and its crystallographic symmetry mate ? Is there a way to switch off symmetry related van der waals terms from the penalty function in phenix.refine ? I have already tried refining by changing the occupancy of PEG to 0.5 but this does not work as after running refinement the PEG molecule is pushed out of the electron density map. Thanks, Chandrika

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Geometry analysis
by Ulrich Baumann 29 Apr '09

29 Apr '09

Hi, I am just wondering whether there is a tool/feature in Phenix that (i) prints out all bonds/angles deviating by some specified number of standard deviations, and (ii) reads a user-defined .cif file for ligands as well so that this ligand appears in (i) as well. Phenix.pdbtools prints a bond histogram and I did not manage to include an external .cif file. Most likely this is easy to do and I haven't found it in the manual yet. Thanks in advance, Ulrich

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fobs-fobs difference electron density maps
by chandra bose 29 Apr '09

29 Apr '09

Hi, I was wondering how to make fobs-fobs difference electron density maps with phenix using data sets from two crystals. I know cns has a script for this... thanks Charlie

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Re: [phenixbb] Exploded ligands and phenix...
by Ralf W. Grosse-Kunstleve 29 Apr '09

29 Apr '09

Hi Ruben, > The cryst1 card of the pdb is the next: > CRYST1 98.500 104.050 415.200 90.00 90.00 90.00 P 21 21 21 I tried phenix.pdbtools --geometry-regularization again after adding this CRYST1 card. The result looks good, i.e. symmetry interactions don't seem to be the problem. > For non-bound interactions the distance is sometimes > less than the VDW-radius. Could this be the problem? No, I don't think so. Your histogram of nonbonded interaction distances looks reasonable. > The log file can be downloaded here: > files.me.com/ruben.vandermeeren/9tuifv Clearly, the .cif file is read, otherwise phenix.refine would stop very early on. Sorry, I still don't know what's going wrong. Could you send me the phenix.refine inputs for debugging (to me directly, not to phenixbb)? Ralf

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Exploded ligands and phenix...
by Ruben Van der Meeren 28 Apr '09

28 Apr '09

Hi, I'm using phenix for the refinement of my protein (phenix.refine). But there is a problem... My protein contains a ligand. For this ligand I use the optimal coordinates wich I downloaded from the HIC-Up server. Then, as coot and phenix need a cif file, I generate a cif file using the PRODRG Server and select (copy-paste) the Refmac5 output --> *.cif . Below you can see the content of this cif file and also the pdb file. Coot can use this cif file. But when I refine the protein (e.g. even only individual sites) the ligand "explodes". In coot you then see only single atoms and no bonds. To illustrate this you can see a pictures on this website: http://gallery.me.com/ruben.vandermeeren#100216 --> "exploded" First I thought that phenix could not find the cif file, but the correct path (via monomers) is given in the parameter file and I also used the command line to import the cif file, but still the ligand "explodes". I use the latest version of phenix for mac (phenix-1.4-3). But more important: I also tried refmac (from ccp4) to refined my protein with it and here there is "no explosion". So refmac does something that phenix doens't: it can refine my protein with the ligand. You can see the nice picture on this website: http://gallery.me.com/ruben.vandermeeren#100216 --> "as it should be". So my question is on how to resolve the issue using phenix.refine. Is phenix somehow unable to read the contents of the cif file? Best regards, Ruben -------------------------------------------------------------------------------------------------------------------------------------------------------- PDB COMPND TRE TREHALOSE; ALPHA-D-GLUCOPYRANOSYL-ALPHA-D-GLUCOPYRANOSIDE REMARK TRE Part of HIC-Up: http://xray.bmc.uu.se/hicup REMARK TRE Extracted from PDB file pdb1j1m.ent REMARK TRE Formula C12 H22 O11 REMARK TRE Nr of non-hydrogen atoms 23 REMARK TRE Eigen-values covariance X/Y/Z 187.8 54.6 26.5 REMARK TRE Residue type TRE REMARK TRE Residue name 7347 REMARK TRE Original residue name (for O) $304 REMARK TRE RESOLUTION. 1.50 ANGSTROMS. REMARK TRE occurs in 21 other PDB entries REMARK TRE Also in <1.5A : 2BHY 2BY2 2BY3 2Z3G REMARK TRE Resolution (A) : 1.50 1.50 1.50 1.50 REMARK TRE Also in 1.5-2.0A : 2BY0 2BY1 2BXY 2BXZ 1EU8 1F0P 2EBF 2CY6 2E4P REMARK TRE Resolution (A) : 1.55 1.55 1.75 1.75 1.90 1.90 1.90 2.00 2.00 REMARK TRE Also in 2.0-2.5A : 2DXY 2FPD 1NI6 2B1Q 1V6A 2E50 2EBH REMARK TRE Resolution (A) : 2.03 2.05 2.10 2.20 2.30 2.30 2.40 REMARK TRE Also in 2.5-3.0A : 1TEX REMARK TRE Resolution (A) : 2.60 REMARK TRE HETATM 1 C1 TRE 7347 1.108 0.876 0.900 1.00 20.00 HETATM 2 C2 TRE 7347 1.959 1.953 0.170 1.00 20.00 HETATM 3 C3 TRE 7347 2.717 1.276 -1.006 1.00 20.00 HETATM 4 C4 TRE 7347 3.662 0.237 -0.355 1.00 20.00 HETATM 5 C5 TRE 7347 2.806 -0.843 0.385 1.00 20.00 HETATM 6 C6 TRE 7347 3.596 -1.917 1.069 1.00 20.00 HETATM 7 O1 TRE 7347 0.133 0.432 0.010 1.00 20.00 HETATM 8 O2 TRE 7347 1.086 2.923 -0.297 1.00 20.00 HETATM 9 O3 TRE 7347 3.472 2.234 -1.665 1.00 20.00 HETATM 10 O4 TRE 7347 4.408 -0.441 -1.302 1.00 20.00 HETATM 11 O5 TRE 7347 1.964 -0.233 1.404 1.00 20.00 HETATM 12 O6 TRE 7347 2.687 -2.806 1.676 1.00 20.00 HETATM 13 C1P TRE 7347 -0.814 -0.557 0.430 1.00 20.00 HETATM 14 C2P TRE 7347 -1.601 -1.752 -0.126 1.00 20.00 HETATM 15 C3P TRE 7347 -2.572 -1.142 -1.231 1.00 20.00 HETATM 16 C4P TRE 7347 -3.557 -0.224 -0.472 1.00 20.00 HETATM 17 C5P TRE 7347 -2.743 0.960 0.225 1.00 20.00 HETATM 18 C6P TRE 7347 -3.666 1.891 1.015 1.00 20.00 HETATM 19 O2P TRE 7347 -0.693 -2.574 -0.755 1.00 20.00 HETATM 20 O3P TRE 7347 -3.323 -2.155 -1.812 1.00 20.00 HETATM 21 O4P TRE 7347 -4.483 0.363 -1.367 1.00 20.00 HETATM 22 O5P TRE 7347 -1.775 0.343 1.115 1.00 20.00 HETATM 23 O6P TRE 7347 -4.371 1.155 1.989 1.00 20.00 REMARK TRE ENDHET -------------------------------------------------------------------------------------------------------------------------------------------------------- CIF # WARNING: REFMAC5 uses columns 77-78 of PDB ATOM records to # establish equivalence between model and topology. If # you use O or other programmes that produce defective # PDB files you must restore these columns, otherwise # REFMAC5 will not recognise this topology. # # # This file was generated by PRODRG version 071121.0636 # PRODRG written/copyrighted by Daan van Aalten # and Alexander Schuettelkopf # # Questions/comments to dava(a)davapc1.bioch.dundee.ac.uk # # When using this software in a publication, cite: # A. W. Schuettelkopf and D. M. F. van Aalten (2004). # PRODRG - a tool for high-throughput crystallography # of protein-ligand complexes. # Acta Crystallogr. D60, 1355--1363. # # global_ _lib_name prodrg_lib _lib_version 71121 _lib_update ? # # --------------- # 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 TRE TRE 'TRE ' non-polymer 45 23 . # # --------------- # data_comp_TRE # 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 TRE O2 O OH1 -0.115 TRE HAA H HOH1 0.028 TRE C2 C CH1 0.074 TRE 1H2 H HCH1 0.000 TRE C3 C CH1 0.074 TRE 1H3 H HCH1 0.000 TRE O3 O OH1 -0.115 TRE HAB H HOH1 0.028 TRE C4 C CH1 0.074 TRE 1H4 H HCH1 0.000 TRE O4 O OH1 -0.115 TRE HAC H HOH1 0.028 TRE C5 C CH1 0.126 TRE 1H5 H HCH1 0.000 TRE C6 C CH2 0.037 TRE 1H6 H HCH2 0.000 TRE 2H6 H HCH2 0.000 TRE O6 O OH1 -0.115 TRE HAD H HOH1 0.028 TRE O5 O O2 -0.109 TRE C1 C CH1 0.126 TRE 1H1 H HCH1 0.000 TRE O1 O O2 -0.109 TRE C1P C CH1 0.126 TRE 1H1P H HCH1 0.000 TRE O5P O O2 -0.109 TRE C5P C CH1 0.126 TRE 1H5P H HCH1 0.000 TRE C6P C CH2 0.037 TRE 1H6P H HCH2 0.000 TRE 2H6P H HCH2 0.000 TRE O6P O OH1 -0.115 TRE HAH H HOH1 0.029 TRE C4P C CH1 0.074 TRE 1H4P H HCH1 0.000 TRE O4P O OH1 -0.115 TRE HAG H HOH1 0.028 TRE C3P C CH1 0.074 TRE 1H3P H HCH1 0.000 TRE O3P O OH1 -0.115 TRE HAF H HOH1 0.028 TRE C2P C CH1 0.074 TRE 1H2P H HCH1 0.000 TRE O2P O OH1 -0.115 TRE HAE H HOH1 0.028 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 TRE O2 n/a C2 START TRE HAA O2 . . TRE C2 O2 C1 . TRE 1H2 C2 . . TRE C3 C2 C4 . TRE 1H3 C3 . . TRE O3 C3 HAB . TRE HAB O3 . . TRE C4 C3 C5 . TRE 1H4 C4 . . TRE O4 C4 HAC . TRE HAC O4 . . TRE C5 C4 O5 . TRE 1H5 C5 . . TRE C6 C5 O6 . TRE 1H6 C6 . . TRE 2H6 C6 . . TRE O6 C6 HAD . TRE HAD O6 . . TRE O5 C5 . . TRE C1 C2 O1 . TRE 1H1 C1 . . TRE O1 C1 C1P . TRE C1P O1 C2P . TRE 1H1P C1P . . TRE O5P C1P C5P . TRE C5P O5P C4P . TRE 1H5P C5P . . TRE C6P C5P O6P . TRE 1H6P C6P . . TRE 2H6P C6P . . TRE O6P C6P HAH . TRE HAH O6P . . TRE C4P C5P C3P . TRE 1H4P C4P . . TRE O4P C4P HAG . TRE HAG O4P . . TRE C3P C4P O3P . TRE 1H3P C3P . . TRE O3P C3P HAF . TRE HAF O3P . . TRE C2P C1P O2P . TRE 1H2P C2P . . TRE O2P C2P HAE . TRE HAE O2P . END TRE O5 C1 . ADD TRE C3P C2P . ADD 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 TRE O2 HAA single 1.000 0.027 TRE O2 C2 single 1.430 0.025 TRE C2 C3 single 1.530 0.025 TRE C2 C1 single 1.530 0.025 TRE C3 O3 single 1.430 0.025 TRE C3 C4 single 1.530 0.025 TRE O3 HAB single 1.000 0.027 TRE C4 O4 single 1.430 0.025 TRE C4 C5 single 1.530 0.025 TRE O4 HAC single 1.000 0.027 TRE C5 C6 single 1.530 0.033 TRE C5 O5 single 1.435 0.033 TRE C6 O6 single 1.430 0.025 TRE O6 HAD single 1.000 0.027 TRE O5 C1 single 1.435 0.033 TRE C1 O1 single 1.435 0.033 TRE O1 C1P single 1.435 0.033 TRE C1P O5P single 1.435 0.033 TRE C1P C2P single 1.530 0.025 TRE O5P C5P single 1.435 0.033 TRE C5P C6P single 1.530 0.033 TRE C5P C4P single 1.530 0.025 TRE C6P O6P single 1.430 0.025 TRE O6P HAH single 1.000 0.027 TRE C4P O4P single 1.430 0.025 TRE C4P C3P single 1.530 0.025 TRE O4P HAG single 1.000 0.027 TRE C3P O3P single 1.430 0.025 TRE C3P C2P single 1.530 0.025 TRE O3P HAF single 1.000 0.027 TRE C2P O2P single 1.430 0.025 TRE O2P HAE single 1.000 0.027 TRE C2 1H2 single 1.000 0.020 TRE C3 1H3 single 1.000 0.020 TRE C4 1H4 single 1.000 0.020 TRE C5 1H5 single 1.000 0.020 TRE C6 1H6 single 1.000 0.020 TRE C6 2H6 single 1.000 0.020 TRE C1 1H1 single 1.000 0.020 TRE C1P 1H1P single 1.000 0.020 TRE C5P 1H5P single 1.000 0.020 TRE C6P 1H6P single 1.000 0.020 TRE C6P 2H6P single 1.000 0.020 TRE C4P 1H4P single 1.000 0.020 TRE C3P 1H3P single 1.000 0.020 TRE C2P 1H2P single 1.000 0.020 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 TRE HAA O2 C2 109.500 3.158 TRE O2 C2 C3 109.500 2.727 TRE O2 C2 C1 109.500 2.727 TRE C3 C2 C1 111.000 2.727 TRE C2 C3 O3 109.500 2.727 TRE C2 C3 C4 111.000 2.727 TRE O3 C3 C4 109.500 2.727 TRE C3 O3 HAB 109.500 3.158 TRE C3 C4 O4 109.500 2.727 TRE C3 C4 C5 111.000 2.727 TRE O4 C4 C5 109.500 2.727 TRE C4 O4 HAC 109.500 3.158 TRE C4 C5 C6 109.500 5.000 TRE C4 C5 O5 109.500 4.412 TRE C6 C5 O5 109.500 4.412 TRE C5 C6 O6 109.500 2.727 TRE C6 O6 HAD 109.500 3.158 TRE C5 O5 C1 109.500 3.750 TRE C2 C1 O5 109.500 4.412 TRE C2 C1 O1 109.500 4.412 TRE O5 C1 O1 109.500 4.412 TRE C1 O1 C1P 109.500 3.750 TRE O1 C1P O5P 109.500 4.412 TRE O1 C1P C2P 109.500 4.412 TRE O5P C1P C2P 109.500 4.412 TRE C1P O5P C5P 109.500 3.750 TRE O5P C5P C6P 109.500 4.412 TRE O5P C5P C4P 109.500 4.412 TRE C6P C5P C4P 109.500 5.000 TRE C5P C6P O6P 109.500 2.727 TRE C6P O6P HAH 109.500 3.158 TRE C5P C4P O4P 109.500 2.727 TRE C5P C4P C3P 111.000 2.727 TRE O4P C4P C3P 109.500 2.727 TRE C4P O4P HAG 109.500 3.158 TRE C4P C3P O3P 109.500 2.727 TRE C4P C3P C2P 111.000 2.727 TRE O3P C3P C2P 109.500 2.727 TRE C3P O3P HAF 109.500 3.158 TRE C1P C2P C3P 111.000 2.727 TRE C1P C2P O2P 109.500 2.727 TRE C3P C2P O2P 109.500 2.727 TRE C2P O2P HAE 109.500 3.158 TRE O2 C2 1H2 109.500 3.300 TRE C2 C3 1H3 109.500 3.300 TRE C3 C4 1H4 109.500 3.300 TRE C4 C5 1H5 109.500 3.300 TRE C5 C6 1H6 109.500 3.300 TRE C5 C6 2H6 109.500 3.300 TRE C2 C1 1H1 109.500 3.300 TRE O1 C1P 1H1P 109.500 3.300 TRE O5P C5P 1H5P 109.500 3.300 TRE C5P C6P 1H6P 109.500 3.300 TRE C5P C6P 2H6P 109.500 3.300 TRE C5P C4P 1H4P 109.500 3.300 TRE C4P C3P 1H3P 109.500 3.300 TRE C1P C2P 1H2P 109.500 3.300 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 TRE var_001 C1 C2 O2 HAA 60.000 13.333 3 TRE CONST_001 C4 C3 C2 O2 60.000 0.714 3 TRE CONST_002 O2 C2 C1 O1 60.000 0.714 3 TRE var_002 C2 C3 O3 HAB 60.000 13.333 3 TRE CONST_003 C5 C4 C3 C2 60.000 0.714 3 TRE var_003 C3 C4 O4 HAC 60.000 13.333 3 TRE CONST_004 C3 C4 C5 O5 60.000 0.714 3 TRE var_004 C4 C5 C6 O6 60.000 2.857 3 TRE CONST_005 C4 C5 O5 C1 60.000 1.111 3 TRE var_005 C5 C6 O6 HAD 60.000 13.333 3 TRE CONST_006 O1 C1 O5 C5 60.000 1.111 3 TRE var_006 C2 C1 O1 C1P 60.000 4.444 3 TRE var_007 C2P C1P O1 C1 60.000 4.444 3 TRE CONST_007 O1 C1P O5P C5P 60.000 1.111 3 TRE CONST_008 O1 C1P C2P O2P 60.000 0.714 3 TRE CONST_009 C4P C5P O5P C1P 60.000 1.111 3 TRE var_008 O5P C5P C6P O6P 60.000 2.857 3 TRE CONST_010 O5P C5P C4P C3P 60.000 0.714 3 TRE var_009 C5P C6P O6P HAH 60.000 13.333 3 TRE var_010 C5P C4P O4P HAG 60.000 13.333 3 TRE CONST_011 C2P C3P C4P C5P 60.000 0.714 3 TRE var_011 C4P C3P O3P HAF 60.000 13.333 3 TRE CONST_012 O2P C2P C3P C4P 60.000 0.714 3 TRE var_012 C1P C2P O2P HAE 60.000 13.333 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 TRE chir_001 C2 O2 C3 C1 positiv TRE chir_002 C3 C2 C4 O3 positiv TRE chir_003 C4 C3 O4 C5 positiv TRE chir_004 C5 C4 O5 C6 positiv TRE chir_005 C1 C2 O5 O1 positiv TRE chir_006 C1P O1 C2P O5P positiv TRE chir_007 C5P O5P C6P C4P positiv TRE chir_008 C4P C5P C3P O4P positiv TRE chir_009 C3P C4P O3P C2P positiv TRE chir_010 C2P C1P O2P C3P positiv # # --------------- # ____________________________________________________________________ Ruben Van der Meeren Bachelor in biochemistry and biotechnology Adress: de Pretlaan 26, B9850 Nevele Tel.: +32478/217480 E-Mail: ruben.vandermeeren(a)mac.com; ruben.vandermeeren(a)ugent.be URL: http://web.mac.com/ruben.vandermeeren iChat: ruben.vandermeeren(a)mac.com Skype: ruben_van_der_meeren

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Optimizing mask parameters for twinned data
by Katya Heldwein 28 Apr '09

28 Apr '09

Hi, is it possible to optimize mask parameters for a model refined with a twinning operator? When I try to do so using optimize_mask=true option, I get the error message: AttributeError: 'twin_model_manager' object has no attribute 'optimize_mask_and_update_solvent_and_scale'. Katya -- Ekaterina Heldwein, Ph.D. Assistant Professor Department of Molecular Biology and Microbiology Tufts University 136 Harrison Ave Boston, MA 02111 phone: 617-636-0858 fax: 617-636-0337 e-mail: katya.heldwein(a)tufts.edu

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fwd: Resolve on Mac
by Nathaniel Echols 27 Apr '09

27 Apr '09

(Forwarded on behalf of James Naismith - I have no idea why the server rejected this message.) Begin forwarded message: > From: James Naismith <naismith(a)st-andrews.ac.uk> > Date: April 23, 2009 9:24:05 AM PDT > To: phenixbb(a)phenix-online.org > Subject: Resolve on Mac > > > This is not a bug but some feature of the new Mac (or perhaps mine > is broken). > > Tom Terwilliger can run the same job on his older Mac and on Linux. > However, with my new Mac resolve complains that it can't allocate > enough memory. > > Since my machine has 8GB of memory and Tom's has 2 GB, it is > something to do with the esetup either Mac or Phenix. > > I am a newbie on the Mac, I wondered if anyone could help me. (Tom > is also new to Mac and agreed to my posting here). > > best > Jim > > > Hardware Overview: > > Model Name: MacBook Pro > Model Identifier: MacBookPro5,2 > Processor Name: Intel Core 2 Duo > Processor Speed: 2.93 GHz > Number Of Processors: 1 > Total Number Of Cores: 2 > L2 Cache: 6 MB > Memory: 8 GB > Bus Speed: 1.07 GHz > Boot ROM Version: MBP52.008E.B00 > SMC Version: 1.42f4 > Serial Number: W89090Y82QT > Sudden Motion Sensor: > State: Enabled > > > > -- > James H. Naismith FRSE | mailto:[email protected] > Professor of Chemical Biology | mailto:[email protected] > (teaching) > Centre for Biomolecular Sciences|Office: (44) or (0) 1334463792 > The North Haugh |Secretary: (44) or (0) 1334463401 > The University Sciences |Fax: (44) or (0) 1334467229 > Fife KY16 9ST U.K. |http://www.st-and.ac.uk/~strucbio > > The University of St Andrews is a charity registered in Scotland : > No SC013532 > > >

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poor phasing
by vennila Natesan 27 Apr '09

27 Apr '09

Dear Tom Thankyou for your kind reply.I checked my data witn phenix.xtriage and there are good anomalous signal (>0.05)in all the resolution shells. Also the systematic absences show it is P43212.Still i couldnt solve using phenix.Where is the thing going wrong? Xtriage results also showed no twinning. My previous message: I am using phenix1.4-4 version. In autosol, got the score of 10.24 for one iodine soaked data. FOM:0.27 and only 54 residues ( that too wrongly) were built out of 129.(CC=0.4), R=0.49 and Rfree=0.574. Regrading the data quality, Rsym:0.0448, Ranom:0.055, Resln:25.0-2.6A Spacegroup is P43212, completeness:99.4%, Multiplicity:11.7, anomalos signal is 1.52 at lowest resoln and higher in high resolution shells. What might be reason for not able to solve this structure?

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observed reflection numbers of refinement greater than the experiment
by carlbluesky＠yahoo.co.jp 24 Apr '09

24 Apr '09

Hi all, I have a problem with reflection numbers of phenix.refine. I did the phenix.refine then i found that the number of observed reflections given for the refinement 75747 (48-2.85A) is greater than the number of observed reflections for the experiment 40434 (50-2.85A). It shoud be around 40000. . This is a peak of MAD data about 2.85A. I used the TLS parameters to refine the structure. I really don't know why because this is my first time use phenix to do refinement. Any advice and suggestion are welcome! Thanks. Carl --------------------------------- Power up the Internet with Yahoo! Toolbar.

3 3

rfree checksums version 1.3 and 1.4
by hari jayaram 24 Apr '09

24 Apr '09

Hi am using the same exact mtz data file from CCP4 uniquefy for two refinements in phenix. I did one round of refinement in phenix 1.3 and then used the output pdb of that refinement and input into the next round of refinement . Only I switched versions to phenix version 1.4. Most other things weere the same including the resolution cutoff used and the input mtz. But phenix tells me that the md5checksums dont match. i am very sure its the same input mtz and identical data resolution ( both cases specifying refinement.input.xray_data.high_resolution=3.0) Could this message of mismatched checksums be an error due to chaging versions midtsream . I certainly dont want to be trampling on my Rfree reflections but apart from copying files to a new directory for the next round and changing phenix versions I have changed little else Thanks for your help in advance hari

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Re: [phenixbb] poor phasing
by vennila Natesan 24 Apr '09

24 Apr '09

Dear members, > > I am using phenix1.4-4 version. In autosol, got the score of 10.24 for one > iodine soaked data. > FOM:0.27 and only 54 residues ( that too wrongly) were built out of > 129.(CC=0.4), R=0.49 and Rfree=0.574. > Regrading the data quality, Rsym:0.0448, Ranom:0.055, Resln:25.0-2.6A > Spacegroup is P43212, completeness:99.4%, Multiplicity:11.7, anomalos > signal is 1.52 at lowest resoln and higher in high resolution shells. > > What might be reason for not able to solve this structure? > >

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viewing previous refinement run validation report
by CK 23 Apr '09

23 Apr '09

Hello all, I am using the phenix 1.4-43 gui to run phenix.refine on my structure and so far I'm very impressed. However, after running a refinement job I had to close the gui before I was finished examining the validation report and now would like to look at it again. Upon relaunching the gui I can't seem to find a way to reload log files/ validation reports from previous runs. Am I missing something obvious here or is the feature not yet implemented? Thanks, Chris

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nightly builds nit (and a question)
by Ben Eisenbraun 21 Apr '09

21 Apr '09

Howdy, I'm not sure you are soliciting bugs on the nightly builds, but I thought I'd mention these. Please let me know if you don't need/want them. I downloaded and installed the 1.4-37 nightly builds. The installations went fine for linux and OS X PPC/x86. There are some absolute symlinks in the installation that don't work: phenix-1.4-37/build/intel-linux-2.6/base/bin/wx-config -> /net/longnose/scratch1/phenix/phenix-1.4-37/build/intel-linux-2.6/base/lib/wx/config/gtk2-ansi-release-2.8 On the OS X there are some that don't appear to matter, e.g.: phenix-1.4-37/build/mac-intel-osx/base/bin/MacPyMOL.app/pymol/test/pdb -> /Volumes/Macintosh HD/Users/delwarl/pdb/entries And some that maybe do: phenix-1.4-37/build/mac-intel-osx/base/bin/python2.6 -> /net/patchnose/scratch1/phenix/phenix-1.4-37/build/mac-intel-osx/base/Python.framework/Versions/2.6/bin/python2.6 Since the nightly builds don't build the ext_ref_files, should I just symlink them to the ones in the 1.4-3 release? Thanks. -ben -- | Ben Eisenbraun | Software Gunky | | Structural Biology Grid | http://sbgrid.org | | Harvard Medical School | http://hms.harvard.edu |

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SA_OMIT map at low resolution
by 邬金 21 Apr '09

21 Apr '09

Hi, I would like to calculate sa_omit map for a low resolution structure (4.0 Ang) to validate the conformation in some regions. What's the proper way to do it? Followed the instruction, I tried: phenix.autobuild data=mydata.mtz model=mybestmodel.pdb omit_box_pdb=mybestmodel.pdb \ omit_res_start_list=100 omit_res_end_list=200 omit_chain_list=L \ composite_omit_type=sa_omit I have several questions: 1. "omit_box_pdb=mybestmodel.pdb": If I define the region that I want to omit, do I need to define the omit_box pdb as well? Should it be complete model or the omit region? 2. I have 4 fold NCS axis, if I want to omit a loop in four copies, how can I define 4 corresponding regions in different chains? e.g omit region: 100-200 in chain L, M, N, O: omit_chain_list = L omit_chain_list = M omit_chain_list = N omit_chain_list = O omit_res_end_list = "200" omit_res_start_list = "100" 3. If I want to omit several loops in one copy, should I turn off NCS? Like: find_ncs=False input_ncs_file= None optimize_ncs=False 4. How to define several omit regions in one chain? Many thanks, Jin _________________________________________________________________ 上Windows Live 中国首页，下载最新版 MSN！ http://im.live.cn/

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Re: [phenixbb] phenixbb Digest, Vol 41, Issue 12
by Ho-Leung Ng 21 Apr '09

21 Apr '09

Hi Zach, You probably have the wrong space group. P3 is rarely represented in the PDB, with only 67 deposited structures out of 57000. You can use Phaser to automatically try all the other P3 related space groups. phenix.xtriage will also try to predict the space group for you. Good luck! Ho UC Berkeley

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phenix.automr high zscore but too many clashes
by zach powers 18 Apr '09

18 Apr '09

Hi, I have a problem and i wonder if someone has had a similar experience. I have been using phenix.automr program to find an MR solution for a protein. When I ask Phaser to use copies=2 I find a number of solutions with poor z-scores (3-4). When I ask it to use copies=3, I get great Z-scores (see below) but no solution due to the high number of clashes (>100!). As an x-ray newbie I am a bit perplexed of what to make of this: the solution is not good because there is not enough space in the unit cell to comfortably accommodate all three molecules yet the Z-score indicates the structure is good. My structure does have several loops and these may be contributing to the clashing residues. As a newbie I have a newbie question - what does this mean (great z-score but no solutions)? Is this non-solution a possible solution if I play with it, or is the packing simply too tight and the Z-scores are not valid? In the meantime I am chopping my protein into sub-domains as recommended in the Phaser documentation, but if anyone has seen something like this before, any suggestions are welcome. thanks zach charlop-powers Packing Table: Space Group P 3 ------------------------------ Solutions accepted if number of clashes = 135 (lowest number of clashes in list) provided this number of clashes <= 10 (maximum number of allowed clashes) # #Clashes # Accepted Annotation 1 188 NO RFZ=20.3 TFZ=18.2 PAK=10 LLG=431 RFZ=18.5 TFZ=10.4 2 156 NO RFZ=20.3 TFZ=18.2 PAK=10 LLG=431 RFZ=18.5 TFZ=10.2 3 151 NO RFZ=20.3 TFZ=18.2 PAK=10 LLG=431 RFZ=18.5 TFZ=9.8 4 146 NO RFZ=20.3 TFZ=18.2 PAK=10 LLG=431 RFZ=18.5 TFZ=9.7 5 187 NO RFZ=20.3 TFZ=18.2 PAK=10 LLG=431 RFZ=16.3 TFZ=10.5 6 202 NO RFZ=20.3 TFZ=18.2 PAK=10 LLG=431 RFZ=18.5 TFZ=9.2 7 170 NO RFZ=20.3 TFZ=18.2 PAK=10 LLG=431 RFZ=18.5 TFZ=9.1 8 144 NO RFZ=20.3 TFZ=18.2 PAK=10 LLG=431 RFZ=16.3 TFZ=10.2 9 177 NO RFZ=20.3 TFZ=18.2 PAK=10 LLG=431 RFZ=18.5 TFZ=9.1 10 153 NO RFZ=20.3 TFZ=18.2 PAK=10 LLG=431 RFZ=18.5 TFZ=8.9 11 150 NO RFZ=20.3 TFZ=18.2 PAK=10 LLG=431 RFZ=18.5 TFZ=8.8 12 217 NO RFZ=20.3 TFZ=18.2 PAK=10 LLG=431 RFZ=18.5 TFZ=8.6 13 182 NO RFZ=20.3 TFZ=18.2 PAK=10 LLG=431 RFZ=18.5 TFZ=8.6 14 135 NO RFZ=20.3 TFZ=18.2 PAK=10 LLG=431 RFZ=18.5 TFZ=8.5 15 175 NO RFZ=20.3 TFZ=18.2 PAK=10 LLG=431 RFZ=18.5 TFZ=8.3 16 159 NO RFZ=20.3 TFZ=18.2 PAK=10 LLG=431 RFZ=18.5 TFZ=8.3 17 192 NO RFZ=20.3 TFZ=18.2 PAK=10 LLG=431 RFZ=18.5 TFZ=8.3 18 165 NO RFZ=20.3 TFZ=18.2 PAK=10 LLG=431 RFZ=16.3 TFZ=9.2 19 169 NO RFZ=20.3 TFZ=18.2 PAK=10 LLG=431 RFZ=16.3 TFZ=9.1 20 158 NO RFZ=20.3 TFZ=18.2 PAK=10 LLG=431 RFZ=18.5 TFZ=8.0 21 173 NO RFZ=20.3 TFZ=18.2 PAK=10 LLG=431 RFZ=18.5 TFZ=8.0 22 154 NO RFZ=20.3 TFZ=18.2 PAK=10 LLG=431 RFZ=16.3 TFZ=8.9 23 206 NO RFZ=20.3 TFZ=18.2 PAK=10 LLG=431 RFZ=18.5 TFZ=7.8 0 accepted of 23 solutions

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phenix.autobuild error
by Andreas Förster 15 Apr '09

15 Apr '09

Hey all, I'm calling phenix.autobuild with the following command: phenix.autobuild data=second_try_33.1.mtz model=second_try_33.1.pdb \ > seq_file=name_139_414.seq ps_in_rebuild=True On my MacBook Pro (OSX 5.6, phenix Version: 1.4, Release tag: 3, cctbx tag: 2008_12_07_1353, Platform: mac-intel-osx osx-10.5.6), I get the following error: Exception RuntimeError: 'maximum recursion depth exceeded while calling a Python object' in <type 'exceptions.KeyError'> ignored 108409888 On a linux box (RHEL 5.2, phenix Version: 1.4, Release tag: 3, cctbx tag: 2008_12_07_1353, Platform: intel-linux-2.6 redhat-e5.2) I get this error: ******************************************************************************** Failed to carry out AutoBuild_build_cycle: child process stderr output: command: 'csh /csb/home/andreas/name/P6big/second_try/autobuild/AutoBuild_run_2_/TEMP0/RUN_FILE_1' tset: standard error: Invalid argument ******************************************************************************** Each time, the script was run on the same set of files residing on the linux box. I either ssh into the machine and run phenix.autobuild in an ssh shell or mount my linux home directory via MacFusion and run phenix.autobuild on the Mac. I haven't tried copying the files to the Mac, but other phenix commands work with the remote data (e.g. phenix.autobuild data=data.mtz solvent_fraction=.6 ps_in_rebuild=True model=coords.pdb maps_only=True) What's the problem? Andreas -- Andreas Förster, Research Associate Paul Freemont & Xiaodong Zhang Labs Department of Biochemistry, Imperial College London http://www.msf.bio.ic.ac.uk

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Twin refinement issues?
by Phil Jeffrey 10 Apr '09

10 Apr '09

While experimenting with twin refinement for a crystal in P321 that approximates P622 to varying extents, I noticed: | twin fraction: 0.59 twin operator: -h,-k,l | A bug, perhaps ? This twin fraction would seem to be unlikely, since twin fractions > 0.5 have no meaning. Since this data does not scale well in p622 compared to some more heavily-twinned datasets on this xtal form I think the twin fraction is certainly less than 0.5. Xtriage estimates: Statistics depending on twin laws ----------------------------------------------------------------- | Operator | type | R obs. | Britton alpha | H alpha | ML alpha | ----------------------------------------------------------------- | -h,-k,l | M | 0.150 | 0.343 | 0.347 | 0.283 | ----------------------------------------------------------------- Unless of course phenix.refine is reporting 2*alpha. Phenix v1.4-3 Intel Mac OSX 10.5.6 This particular run with: phenix.refine model-08.pdb pz7e_truncate-unique.mtz refinement.main.ncs=true strategy=individual_sites+group_adp --overwrite xray_data.r_free_flags.generate=True twin_law="-h,-k,l" This is a very early non-finessed model. Phil Jeffrey Princeton

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optimize weighs
by Yusuf Akhter 09 Apr '09

09 Apr '09

Dear all, I am refining a protein structure using phenix.refine, when i tried to use optimize_wxc, optimize_wxu It always crashes and gives following error. May anybody can explain what is the problem?? Traceback (most recent call last): File "/public/xtal/phenix/phenix-1.3b/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 "/public/xtal/phenix/phenix-1.3b/phenix-1.3b/phenix/phenix/refinement/command_line.py", line 78, in run call_back_after_monitor_collect=call_back_after_monitor_collect) File "/public/xtal/phenix/phenix-1.3b/phenix-1.3b/phenix/phenix/refinement/driver.py", line 1308, in run log = log) File "/public/xtal/phenix/phenix-1.3b/phenix-1.3b/phenix/phenix/refinement/strategies.py", line 642, in refinement_machine log = log) File "/public/xtal/phenix/phenix-1.3b/phenix-1.3b/phenix/phenix/refinement/weight_xray_chem.py", line 327, in __init__ self.wxc_optimization() File "/public/xtal/phenix/phenix-1.3b/phenix-1.3b/phenix/phenix/refinement/weight_xray_chem.py", line 450, in wxc_optimization rw, rf, b, a, a_xc = self.wx_opt_helper(w = wxc_scale_0 * wxc, sites=True) File "/public/xtal/phenix/phenix-1.3b/phenix-1.3b/phenix/phenix/refinement/weight_xray_chem.py", line 387, in wx_opt_helper verbose = 0) TypeError: __init__() takes at least 5 non-keyword arguments (3 given) Thanks in advance. Yusuf

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twin refinement error
by jonathan elegheert 08 Apr '09

08 Apr '09

Dear Phenix developers, I am rigid-body refining a PM-twinned structure (C2221 => P6x22) with the operators suggested from xtriage or SFcheck but I keep running into this same error (version 1.4.3 or latest cci aps bundles); 1/2*h-1/2*k,-3/2*h-1/2*k,-l 1/2*h+1/2*k,3/2*h-1/2*k,-l Any suggestions as to how I can resolve this? Many thanks in advance, Jonathan Elegheert PhD student Ghent University Belgium ------------------------------------------------------------------------- Traceback (most recent call last): File "/usr/local/cciapps/cci_apps_sources/phenix/phenix/command_line/refine.py", line 16, in <module> command_line.run(command_name="phenix.refine", args=sys.argv[1:]) File "/usr/local/cciapps/cci_apps_sources/phenix/phenix/refinement/command_line.py", line 89, in run call_back_after_monitor_collect=call_back_after_monitor_collect) File "/usr/local/cciapps/cci_apps_sources/phenix/phenix/refinement/driver.py", line 1121, in run call_back_after_monitor_collect = call_back_after_monitor_collect) File "/usr/local/cciapps/cci_apps_sources/phenix/phenix/refinement/strategies.py", line 190, in refinement_machine twin_law = sgtbx.rt_mx( params.twinning.twin_law ) RuntimeError: cctbx InternalError: /net/garter/scratch1/rwgk/auto_build/sources/cctbx/sgtbx/rt_mx.cpp(230): Unsuitable value for rational rotation matrix.

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Phenix.refine Rigid Body multi_body_factor
by Mary Fitzgerald 08 Apr '09

08 Apr '09

I was wondering when you would want to change multi_body_factor= 1? Is this something you would change when you have multiple rigid body domains? From the name, that's what I'm guessing it's for. I'm refining a large over 400 kD multimer complex with two complexes in the ASU. So, if I have 5 chains in each multimer would I want to try to change the multi_body_factor to 10? Or does multi_body_factor affect something else. Thanks, Mary X. Fitzgerald Postdoctoral Associate Arnold Lab

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optimize_wxc and wxu
by Scott Classen 08 Apr '09

08 Apr '09

Hello phenixbb, In general should one optimize wxc and wxu ONLY as a final polishing step or can this be done earlier in the refinement and then the optimized values used for subsequent rounds of refinement? If so which values in the log file should be written into the .def file and where? Here is a snippit from my def file after I optimized weights and changed the optimize flags back to False: target_weights { mode = *automatic every_macro_cycle wxc_scale = 0.5 wxu_scale = 1 wc = 1 wu = 1 fix_wxc = None fix_wxu = None optimize_wxc = False bonds_rmsd_max = 0.05 angles_rmsd_max = 3.5 optimize_wxu = False shake_sites = True shake_adp = 10 regularize_ncycles = 50 verbose = 1 wnc_scale = 0.5 wnu_scale = 1 rmsd_cutoff_for_gradient_filtering = 3 } Thanks, Scott ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Scott Classen, Ph.D. SIBYLS Beamline 12.3.1 http://bl1231.als.lbl.gov Advanced Light Source Lawrence Berkeley National Laboratory 1 Cyclotron Rd MS6R2100 Berkeley, CA 94720 C) 510.206.4418 O) 510.495.2697 Beamline) 510.495.2134 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

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restrains for nucleaic acid base pairs
by Imre Toeroe 08 Apr '09

08 Apr '09

Hi, Does anybody know an easy way to restrain nucleic acid base pairs (base stacking+Watson-Crick base pairing) in phenix.refine? I am refining against a 3.3 A dataset. Thanks, Imre

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phenix autobuild and omit map
by rpai＠berkeley.edu 07 Apr '09

07 Apr '09

Hi, I have a loop that was improperly built when I ran autobuild. the density according to the Fobs-Fcalc maps is not that great. Someone told me that autobuild can use omit maps to build / rebuild the loops so you dont have to do it by hand. Looking at the manual, I found the command, but am a little confused. The model used is the entire model correct? the target.pdb is the chain or region that was not correctly built. For iterative building...how many cycles should I go for? phenix.autobuild data=w1.sca model=coords.pdb omit_box_pdb=target.pdb \ composite_omit_type=iterative_build_omit thanks Raj

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imaginary map (anomlous difference Fourier) from phenix
by Ulrich Baumann 06 Apr '09

06 Apr '09

Hi everybody, I used phenix for calculating anomalous Fourier coefficients (script below) and I get the desired file containing columns FANOM PHANOM. When I read this into Coot for displaying the imaginary map, I only get noise, regardless of resolution cutoff etc. When I export the Fcalcs as CNS format and use CNS for the map calculation, I get very high peaks (i.e. excellent signal-to-noise ratio) on the anomalous scatterers. Inspection of the phenix fcalc file reveals that FOFCWT_no_fill equals FANOM and PHFOFCWT_no_fill is identical to PHANOM . Obviously I am doing something stupidly wrong. Setting xray_data.force_anomalous_flag_to_be_equal_to=true doesn't change anything, by the way, and i am using the latest Phenix version. I vaguely remember that there were an issue with anomlous data but can't find the thread. Thank you very much in advance for enlightening me, Ulrich # source /usr/local/phenix-1.4-3/phenix_env phenix.refine m226h1_rfree-unique.mtz m226h1_hkl2000_6_waters_001.pdb main.number_of_macro_cycles=1 \ refinement.input.xray_data.labels="F(+),SIGF(+),F(-),SIGF(-)" \ xray_data.high_resolution =3.5 strategy=none export_final_f_model=cns output.prefix=sfcalc --overwrite * Space group = 'P3121' (number 152) The mapcoeff.mtz looks like OVERALL FILE STATISTICS for resolution range 0.000 - 0.319 ======================= Col Sort Min Max Num % Mean Mean Resolution Type Column num order Missing complete abs. Low High label 1 ASC 0 49 0 100.00 23.7 23.7 88.43 1.77 H H 2 NONE 0 28 0 100.00 8.4 8.4 88.43 1.77 H K 3 NONE -69 69 0 100.00 0.6 26.2 88.43 1.77 H L 4 NONE 0.0 2220.8 0 100.00 235.55 235.55 88.43 1.77 F 2FOFCWT 5 NONE -180.0 180.0 0 100.00 2.65 89.99 88.43 1.77 P PH2FOFCWT 6 NONE 0.0 956.4 0 100.00 72.48 72.48 88.43 1.77 F FOFCWT 7 NONE -180.0 180.0 0 100.00 2.16 89.97 88.43 1.77 P PHFOFCWT 8 NONE 0.0 2202.8 117 99.84 234.51 234.51 37.16 1.77 F 2FOFCWT_no_fill 9 NONE -180.0 180.0 117 99.84 2.78 89.99 37.16 1.77 P PH2FOFCWT_no_fill 10 NONE 0.0 961.2 117 99.84 72.39 72.39 37.16 1.77 F FOFCWT_no_fill 11 NONE -180.0 180.0 117 99.84 2.19 89.95 37.16 1.77 P PHFOFCWT_no_fill 12 NONE 0.0 961.2 117 99.84 72.39 72.39 37.16 1.77 F ANOM 13 NONE -180.0 180.0 117 99.84 2.19 89.95 37.16 1.77 P PHANOM No. of reflections used in FILE STATISTICS 72570 1 1 3 88.81 -133.90 400.50 -133.90 139.90 -134.31 502.82 -134.31 502.82 -134.31 1 1 4 719.55 109.38 336.98 109.38 703.51 104.61 304.13 104.61 304.13 104.61 1 1 5 987.30 124.20 664.11 124.20 985.68 119.49 659.96 119.49 659.96 119.49 1 1 6 871.35 35.76 152.79 35.76 894.80 36.84 198.58 36.84 198.58 36.84 1 1 7 425.64 38.73 189.77 38.73 419.88 34.24 177.78 34.24 177.78 34.24 1 1 8 406.00 -154.97 53.51 25.03 416.82 -153.85 32.47 26.15 32.47 26.15 1 1 9 73.73 139.84 441.04 139.84 92.83 139.16 479.45 139.16 479.45 139.16

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