How to use grade to get BUSTER restraints for a covalently bound ligand, advanced example 1b0e/SEI

obabel  SEISER_libcheck.pdb -O  SEISER_libcheck.mol2
1 molecule converted
./covalent_grade_create_linkdic.pl  -icif grade-SEI.cif -odic grade-SEISER-link.dic -3let SER -aatnam OG -latnam C71
# covalent_grade_create_linkdic.pl
# use -man option to see full copyright information
# Converting dictionary grade-SEI.cif with refmacdict2tnt resulted in 329 lines starting GEOMETRY, for residue type SEI
# three letter code for amino acid that is modified is SER
# success identified 9 link type restraints and have written them to file grade-SEISER-link.dic
cat grade-SEISER-link.dic
# tnt dictionary to link amino acid SER atom OG
# to ligand SEI atom C71 using restraint type ZSEI
# produced by covalent_grade_create_linkdic.pl jiffy
CATEGORY_AT SER SER
CATEGORY_AT SEI SEI
CONNECT_AT SER OG SEI C71 ZSEI
GEOMETRY ZSEI BOND 1.382 0.030 OG +C71
GEOMETRY ZSEI ANGLE 105.9 3.0 OG +C71 +C59
GEOMETRY ZSEI ANGLE 115.0 3.0 OG +C71 +O74
GEOMETRY ZSEI ANGLE 103.8 3.0 OG +C71 +C73
GEOMETRY ZSEI ANGLE 121.6 3.0 CB OG +C71
GEOMETRY ZSEI TORSION 10000.0 1000000.0 +C59 +C71 OG CB
GEOMETRY ZSEI TORSION 10000.0 1000000.0 +C71 OG CB CA
GEOMETRY ZSEI CHIRAL 1 1 +C71 OG +C73 +O74
LINK         OG  SER A 195                 C71 SEI A 260     1555   1555  1.49  
LINK         OG  SER A 195                 O74 SEI A 260     1555   1555  2.04  
hydrogenate -p 1b0e_correct_link.pdb -o 1b0e_cl_addh.pdb -l grade-SEI.cif
hydrogenate uses the 'reduce' tool; if you publish work which uses it,
please cite

Word, et. al. (1999) J. Mol. Biol. 285, 1735-1747.
For more information see http://kinemage.biochem.duke.edu
Producing CONECT records suitable for molprobity.reduce on SEI
Residues  CA  not hydrogenated; give dictionaries (with the -l dic1 dic2 ... option) to do this
MakeLINK -p 1b0e_cl_addh.pdb  -o 1b0e_cl_addh.seq -d grade-SEISER-link.dic
refine -p 1b0e_cl_addh.pdb -m 1b0e.mtz -Seq 1b0e_cl_addh.seq \
-l grade-SEI.cif -l grade-SEISER-link.dic -d 1b0e_01_gradecovalent_maponly \
-M MapOnly > 1b0e_01_gradecovalent_maponly.log
WARNING: (chiral) Have         1 chiral atoms that are inverted:
WARNING: (chiral)     A|260:C71(SEI)
GEOMETRY ZSEI CHIRAL 1 1 +C71 OG +C73 +O74
GEOMETRY ZSEI CHIRAL 1 1 +C71 OG +O74 +C73
refine -p 1b0e_cl_addh_h741.pdb -m 1b0e_cv_corrected.mtz \
 -Seq 1b0e_cl_addh.seq -l grade-SEI.cif -l grade-SEISER-link-correct-chiral.dic  \
 -d 1b0e_02_refine > 1b0e_02_refine.log

Page by Oliver Smart original version 06 June 2012. Address problems, corrections and clarifications to buster-develop@globalphasing.com