As explained in $BDG_home/docs/gelly/manual/gelly5.html, BUSTER allows users to manually setup utility distance restraints in order to prevent atoms drifting from special positions or symmetry axes. The use of these restraints is illustrated in 2012_06_consortium_special_position.pdf
We can fetch the structure and reflection data with
fetch_PDB 5CMQ
and change into the resulting subdirectory with
cd 5CMQ
To get a list of atoms on special positions as defined by REMARK 375, we can run
grep "REMARK 375 " 5cmq.pdb
which shows us several Zn and waters being on special positions:
REMARK 375 ZN ZN A 203 LIES ON A SPECIAL POSITION. REMARK 375 ZN ZN A 204 LIES ON A SPECIAL POSITION. REMARK 375 ZN ZN A 205 LIES ON A SPECIAL POSITION. REMARK 375 ZN ZN A 206 LIES ON A SPECIAL POSITION. REMARK 375 ZN ZN A 207 LIES ON A SPECIAL POSITION. REMARK 375 HOH A 319 LIES ON A SPECIAL POSITION. REMARK 375 HOH A 519 LIES ON A SPECIAL POSITION. REMARK 375 HOH A 520 LIES ON A SPECIAL POSITION. REMARK 375 HOH A 531 LIES ON A SPECIAL POSITION. REMARK 375 HOH A 534 LIES ON A SPECIAL POSITION. REMARK 375 HOH A 539 LIES ON A SPECIAL POSITION.
using that information, we create a file special.dat containing
NOTE BUSTER_DISTANCE +0.001 0.02 A|203:ZN A|203:ZN SYMM NOTE BUSTER_DISTANCE +0.001 0.02 A|204:ZN A|204:ZN SYMM NOTE BUSTER_DISTANCE +0.001 0.02 A|205:ZN A|205:ZN SYMM NOTE BUSTER_DISTANCE +0.001 0.02 A|206:ZN A|206:ZN SYMM NOTE BUSTER_DISTANCE +0.001 0.02 A|207:ZN A|207:ZN SYMM NOTE BUSTER_DISTANCE +0.001 0.02 A|319:O A|319:O SYMM NOTE BUSTER_DISTANCE +0.001 0.02 A|519:O A|519:O SYMM NOTE BUSTER_DISTANCE +0.001 0.02 A|520:O A|520:O SYMM NOTE BUSTER_DISTANCE +0.001 0.02 A|531:O A|531:O SYMM NOTE BUSTER_DISTANCE +0.001 0.02 A|534:O A|534:O SYMM NOTE BUSTER_DISTANCE +0.001 0.02 A|539:O A|539:O SYMM
that we will use during refinement:
refine -p 5cmq.pdb -m 5cmq.mtz -Gelly special.dat -d 01 | tee 01.lis
As a comparison: what happens with or without those additional restraints (using BUSTER stable 20160324)?
Atom | without restraints | with restraints |
ZN A 203 | ![]() |
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ZN A 205 | ![]() |
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