[buster-discuss] modified amino acid residue in chain

[Clemens Vonrhein]

Hi Wolfram,

On Tue, May 03, 2016 at 10:04:33AM -0400, wtempel wrote:
> refine stops after printing this
> 
>         1 dist=   1.34 idealD=   3.35 sigma=   0.20 abs(Delta/sigma)=   10.07
>           Between atoms   D|51:C (SER)            and   D|52:N (TYC)
>          (C-N)
>  [check-047]
>    ERROR: Between 'N ' and 'C ' atoms. It is possible restraints have not been
>           properly setup. Probably have a residue that should be regarded as a
>           AAREST???
> 
> to ./01-BUSTER/Cycle-1/gelly_sanity_test.lis. I have this feeling that I
> probably *do* have a residue that should be regarded as a AAREST

Yes (the text could probably be improved here): there is a C-N
distance between residues that look both like amino-acid residues with
a distance that is sugggesting a peptide linkage.
 
> as TYC is just the amide of tyrosine and terminates my peptide. But what
> does it mean, and how do I make autobuster regard TYC as “AAREST”?
> I appreciate any help or link to documentation.

Maybe you are missing the correct LINK cards in your PDB file (that
describe the bond between D|51:C (SER) and D|52:N (TYC))?

The easiest to check is

 (1) create the so-called TNT sequence file by hand via

       MakeLINK -p your.pdb -o your.seq

 (2) edit the resulting your.seq file and make sure you have something
     like

       RESIDUE D|51 SER 52    PEPTIDE
       RESIDUE D|52 TYC ENDA  CTERM

 (3) run BUSTER with

       refine -p your.pdb ... -Seq your.seq ...

Does that work for you?

Getting the connectivity description correct when encountering
modified amino-acid residues (or RNA residues for that matter) can be
slightly complicated - especially when the starting model is still
"geometrically challenged" (yours doesn't look like it though).
However, the good thing is that you only need to do that once and you
can re-use the same *.seq file from then on (unless you start adding
more residues to your model).

Cheers

Clemens

-- 

*--------------------------------------------------------------
* Clemens Vonrhein, Ph.D.     vonrhein AT GlobalPhasing DOT com
* Global Phasing Ltd., Sheraton House, Castle Park 
* Cambridge CB3 0AX, UK                   www.globalphasing.com
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