BusterExampleSpecial

BUSTER Example Application: handling special position ions and atoms

• Introduction
• 5CMQ example (atoms on special positions)

Introduction

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

5CMQ example (atoms on special positions)

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	(small movemement away from symmetry axis)	(exactly on symmetry axis)
ZN A 205	(pushed off symmetry axis)	(exactly on symmetry axis)