[phenixbb] how to make covelent link of BME with Cys and refine
Nigel Moriarty
nwmoriarty at lbl.gov
Fri Feb 15 14:57:43 PST 2013
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 <
Rajeshwer.Sankhala at jefferson.edu> 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*
>
> **
>
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>
>
--
Nigel W. Moriarty
Building 64R0246B, Physical Biosciences Division
Lawrence Berkeley National Laboratory
Berkeley, CA 94720-8235
Phone : 510-486-5709 Email : NWMoriarty at LBL.gov
Fax : 510-486-5909 Web : CCI.LBL.gov
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