Hi leo, Thanks for the quick reply, but I don't use SA in my refinement. So that isn't the problem... it must be something else. Best Regards, Ruben Citeren junfeng liu :

Hi Ruben, This is always happened to build ligand into the poor electron density when the SA is on during refinement. I always add ligand in the last refinement cycle without SA. That does work for me. Good luck! leo Ruben Van der Meeren wrote:

...

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 [email protected] # # 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: [email protected]; [email protected] URL: http://web.mac.com/ruben.vandermeeren iChat: [email protected] Skype: ruben_van_der_meeren

_______________________________________________ phenixbb mailing list [email protected] http://www.phenix-online.org/mailman/listinfo/phenixbb

_______________________________________________ phenixbb mailing list [email protected] http://www.phenix-online.org/mailman/listinfo/phenixbb

Hi leo, Thanks for the quick reply, but I don't use SA in my refinement. So that isn't the problem... it must be something else. Best Regards, Ruben Citeren junfeng liu :

Hi Ruben, This is always happened to build ligand into the poor electron density when the SA is on during refinement. I always add ligand in the last refinement cycle without SA. That does work for me. Good luck! leo Ruben Van der Meeren wrote:

...

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 [email protected] # # 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: [email protected]; [email protected] URL: http://web.mac.com/ruben.vandermeeren iChat: [email protected] Skype: ruben_van_der_meeren

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Hi leo, Thanks for the quick reply, but I don't use SA in my refinement. So that isn't the problem... it must be something else. Best Regards, Ruben Citeren junfeng liu :

Hi Ruben, This is always happened to build ligand into the poor electron density when the SA is on during refinement. I always add ligand in the last refinement cycle without SA. That does work for me. Good luck! leo Ruben Van der Meeren wrote:

...

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 [email protected] # # 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: [email protected]; [email protected] URL: http://web.mac.com/ruben.vandermeeren iChat: [email protected] Skype: ruben_van_der_meeren

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Hi Ralf, The coordinates of the ligand in the file I use for refinement are similar to those I posted. I uploaded an overlay of the original ligand and the ligand in my model. Green is model, blue is original... You can see the picture on this site: http://gallery.me.com/ruben.vandermeeren/100216 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 The structure has 4 monomers in which I modeled a ligand monomer A and B. I also checked the .geo file. In most cases (for bonds and Angles) the model is almost equal to the ideal. For dihedrals there is much more disagreement. E.g. for one dihedral the model is 168° whereas the ideal is -60°. For non-bound interactions the distance is sometimes less than the VDW-radius. Could this be the problem? But this is in fact the thing I want to refine. The log file can be downloaded here: files.me.com/ruben.vandermeeren/9tuifv Ruben Citeren "Ralf W. Grosse-Kunstleve" :

Hi Ruben,

...

I'm using phenix for the refinement of my protein (phenix.refine). But there is a problem...

Your pdb and cif file seem OK after a quick check (phenix.pdbtools --geometry-regularization tre.pdb tre.cif). My best guess is that the ligand conincides with a symmetry operation. Are the coordinates in the pdb file you posted similar to the coordinates in the file you used for refinement? Could you send me the CRYST1 card? The phenix.refine log would also be helpful. Note that all geometry restraints are listed in the .geo file written by phenix.refine. Look for nonbonded interactions involving your ligand.

Ralf _______________________________________________ phenixbb mailing list [email protected] http://www.phenix-online.org/mailman/listinfo/phenixbb

Hi Maia, I assume that it is phenix. Because when I refine with refmac5, the ligand doesn't explode. I too had such problems in coot as you describe, but these are fixed now. The cif file was corrupted. So when I used "real space refine zone" in coot the ligand break up (what in fact happen, is that coot doesn't show the bond if it is deviates too far from normal e.g. 2A in stead of 1.5A, but pymol does which give this kind of strange structures: http://gallery.me.com/ruben.vandermeeren#100216 --> "pymol version of exploded ligand"). This problem of the cif file is solved now (using the PRODRG server). And as Ralf said, this "new" cif file seems to be correct. But is there a change that phenix cannot read the cif file properly? Ruben Citeren Maia Cherney :

Hi Ruben

are you sure that it's a phenix problem? Did you try other programs to see your ligand after refinement? I have seen a similar problem in coot with DNA. Coot would break up a DNA when we tried to regularize it, due to a different letter code convention for nucleotides. But when we changed A to Ad, G to Gd etc, there were no problems.

Maia

Ruben Van der Meeren wrote:

...

Hi Ralf,

The coordinates of the ligand in the file I use for refinement are similar to those I posted. I uploaded an overlay of the original ligand and the ligand in my model. Green is model, blue is original... You can see the picture on this site:

http://gallery.me.com/ruben.vandermeeren/100216

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

The structure has 4 monomers in which I modeled a ligand monomer A and B. I also checked the .geo file. In most cases (for bonds and Angles) the model is almost equal to the ideal. For dihedrals there is much more disagreement. E.g. for one dihedral the model is 168° whereas the ideal is -60°. For non-bound interactions the distance is sometimes less than the VDW-radius. Could this be the problem? But this is in fact the thing I want to refine.

The log file can be downloaded here: files.me.com/ruben.vandermeeren/9tuifv

Ruben

Citeren "Ralf W. Grosse-Kunstleve" :

...

Hi Ruben,

...

I'm using phenix for the refinement of my protein (phenix.refine). But there is a problem...

Your pdb and cif file seem OK after a quick check (phenix.pdbtools --geometry-regularization tre.pdb tre.cif). My best guess is that the ligand conincides with a symmetry operation. Are the coordinates in the pdb file you posted similar to the coordinates in the file you used for refinement? Could you send me the CRYST1 card? The phenix.refine log would also be helpful. Note that all geometry restraints are listed in the .geo file written by phenix.refine. Look for nonbonded interactions involving your ligand.

Ralf _______________________________________________ phenixbb mailing list [email protected] http://www.phenix-online.org/mailman/listinfo/phenixbb

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