Raj You should look in the .geo file to see if there is a bond as you can't REALLY tell from the .pdb. I wrote a simple script elbow.refine_geo_display model.geo BME CYS will tell you if it worked. I will take a look if you send the files directly to me. Nigel NB. Any files sent to me will be held in strictest confidence. On Fri, Feb 15, 2013 at 2:04 PM, Rajeshwer Sankhala < [email protected]> wrote:

*Hello Nat,*

**

*Thank you so much for your suggestion. I did run phenix refinement in nightly build phenix version with "*

*intra_chain = True " command. This time refinement worked but again in out put pdb no disulfide bond is estabilished between cys and BME. I provided .pdb, .mtz and .cif files as input. Well can you please suggest me how i can provide both BME and Cys-BME (SS bond) restrains in .cif file? if that happens then i feel refinement should work. I am attaching my .cis file below please have a look and tell me if anything wrong with this?*

BME.cif

# electronic Ligand Builder and Optimisation Workbench (eLBOW) # - a module of PHENIX version 1.8.1-1168 (Mon Sep 28 16:48:00 2012) # - file written: Sat Jan 26 17:25:31 2013 # # Input file: Ref226_154-331-VLD2-BME.pdb # Random seed: 3628800 # Residue: BME # 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 BME BME 'Unknown ' ligand 10 4 . # data_comp_BME # 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 BME S S S2 . -19.3229 -20.3986 17.2400 BME H5 H H . -18.1988 -20.0550 17.0819 BME C1 C CH2 . -19.3558 -21.8852 18.1928 BME H3 H HCH2 . -18.8480 -21.7572 19.0093 BME H4 H HCH2 . -18.9637 -22.6079 17.6781 BME C C CH2 . -20.7668 -22.2261 18.5333 BME H1 H HCH2 . -21.1200 -21.5643 19.1482 BME H2 H HCH2 . -20.7965 -23.1021 18.9488 BME O O OH1 . -21.5280 -22.2370 17.3822 BME H H HOH1 . -22.3435 -22.5247 17.5704 # 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 BME S H5 single 1.186 0.020 BME S C1 single 1.766 0.020 BME C1 H3 single 0.970 0.020 BME C1 H4 single 0.970 0.020 BME C1 C single 1.491 0.020 BME C H1 single 0.970 0.020 BME C H2 single 0.970 0.020 BME C O single 1.380 0.020 BME O H single 0.885 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 BME C1 S H5 109.48 3.000 BME C C1 H4 109.47 3.000 BME C C1 H3 109.47 3.000 BME H4 C1 H3 109.47 3.000 BME C C1 S 109.47 3.000 BME H4 C1 S 109.47 3.000 BME H3 C1 S 109.47 3.000 BME O C H2 109.47 3.000 BME O C H1 109.47 3.000 BME H2 C H1 109.47 3.000 BME O C C1 109.47 3.000 BME H2 C C1 109.47 3.000 BME H1 C C1 109.47 3.000 BME H O C 109.48 3.000 # 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 BME Var_01 O C C1 S 52.25 30.0 3 BME Var_02 H1 C C1 S -67.75 30.0 3 BME Var_03 H2 C C1 S 172.25 30.0 3 BME Var_04 O C C1 H3 172.25 30.0 3 BME Var_05 O C C1 H4 -67.75 30.0 3 # loop_ _chem_link.id _chem_link.comp_id_1 _chem_link.mod_id_1 _chem_link.group_comp_1 _chem_link.comp_id_2 _chem_link.mod_id_2 _chem_link.group_comp_2 _chem_link.name CYS-BME CYS DEL-HG . BME DEL-HS . SS-bridge #

**

**

*Thanks*

**

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

-- Nigel W. Moriarty Building 64R0246B, Physical Biosciences Division Lawrence Berkeley National Laboratory Berkeley, CA 94720-8235 Phone : 510-486-5709 Email : [email protected] Fax : 510-486-5909 Web : CCI.LBL.gov