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

[Clemens Vonrhein]

Dear Mark,

If the problem contact is indeed e.g. between B121 (A conformer) and
E2, you will need the line

  EXCLUDE B|121 E|2

It seems as if none of the examples you tried actually includes the
exact interacting residues? Or am I missing something?

Another possibility is to work with the alternate conformation
identifier. E.g. if you have something where

  (1) a amino-acid residue exists in two alternate conformations A and
      B

  (2) the ligand is only present when this residue is in the B
      conformation and occupies (to some extent) the location of the A
      conformer position

the best thing would be to also set the altConf identifier for the
ligand to B (no need to also have a A conformer). The benefit of using
the correct pattern of altConf identifiers is that only atoms with the
same altConf identifier (or none) "see" each other - and atoms with
different (non-" ") altConf identifiers are invisible to each other
... so no need for an exclude card.

Of course, if you have just built this region htere might indeed be
some poor non-bondend contact and thte exclude cards are required, but
for the final refinement this should no longer be the case.

Does that help?

Cheers

Clemens

PS: and after running "pdb2occ" agains the PDB file you would also
    have a set of occupancy refinement commands to get started with
    refining alternate side-chain conformations where one conformation
    is associated with a ligand structure and the other with
    solvent/water molecules - all nicely restrained to add up to a
    combined occupancy of one as expected (if the model is able to
    completely describe the local situation).



On Thu, Apr 09, 2020 at 03:39:14PM +0000, Mark Roe wrote:
> 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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* Clemens Vonrhein, Ph.D.     vonrhein AT GlobalPhasing DOT com
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