[buster-discuss] Excluding bonding terms between disordered residues.

[Mark Roe]

Hi,

I am having trouble excluding bonding terms between a partially bound ligand and a disordered side chain. I used (several years ago) to just type

EXCLUDE D|121 E|1

At the bottom of the restraints.dat (the molprobity CB deviation fixer) file and this seemed to work, but now it gets ignored and the two residues are forced apart, rather than overlapping.

I also tried to add it directly on the command line with

refine -m ………. -p refine refine-coot-0.pdb ExcludeBadContacts="EXCLUDE A|121 E|2; EXCLUDE B|121 E|1; EXCLUDE B|281 D|281"

but again this is ignored.

 WARNING : some warning messages received - details below

          WARNING: Have |delta/sigma| deviations > 5.0 sigma. Number of outliers for each term:
          WARNING:         1 bond lengths. Worst is     8.0 sigs     1.49 Angs A|283:C.B(GLU)=A|284:N(PRO)
          WARNING:         5 bond angles.  Worst is     7.6 sigs   130.73 degs A|283:C.B(GLU)=A|284:N(PRO)=A|284:CA(PRO)
          WARNING:         1 planes.       Worst is     6.4 sigs     0.13 Angs E|1:C3=C4=N2=C5 (LIG)
          WARNING:        21 idealD contacts. Worst    15.9 sigs     1.41 Angs B|121:CZ.A(TYR)=E|2:C7(LIG)
          WARNING:         4 Bcorrel.      Worst is     9.7 sigs   -24.12 Angs^2 B|3:CA=CB (ALA)
          WARNING: Could be a bad contact but may well be an unrecognized link from
          protein to HETATM residue? It is possible restraints have not been
          properly set up.
          If you want BUSTER to regard this as a bond try adding the
          following card before the CRYST1 line in the input pdb file:
          LINK         CE1ATYR B 121                 C7  LIG E   2     1555   1555  1.67
          WARNING: Could be a bad contact but may well be an unrecognized link from
          protein to HETATM residue? It is possible restraints have not been
          properly set up.
          If you want BUSTER to regard this as a bond try adding the
          following card before the CRYST1 line in the input pdb file:
          LINK         OH ATYR B 121                 C7  LIG E   2     1555   1555  1.68

Can you point me to the relevant part of the manual or explain how I should set this up?


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