[buster-discuss] AdjustModifiedNucleotides

[ClAuS Flensburg]

Hi Ed,

On Tue, Aug 21, 2018 at 05:27:08PM -0400, Edwin Pozharski wrote:
> Hello,
> 
> could someone confirm that AdjustModifiedNucleotides option actually
> works?  

it does ... for the helper program pdb2seq. However, the default
method to generate the sequence file within BUSTER is to use the
alternative helper: MakeLINK.

> IIUC, it is supposed to tell tnt to treat residues that contain
> proper sugar-phosphate atom names as DNA/RNA.  I have some modified
> nucleotides and always get Gelly sanity check error telling me that there
> is bad contact between its P/O3' and preceding/following nucleotide O3'/P.
> The issue can be resolved by adding proper LINK records to the input PDB
> file, but shouldn't this be unnecessary given
> that AdjustModifiedNucleotides defaults to "yes"?

as an alternative to adding the LINK records you should be able to
generate the sequence file using pdb2seq first eg.

    % pdb2seq -p model.pdb -o model.seq
    % refine -m data.mtz -p model.pdb -Seq model.seq ...

but, yes, better would be to have MakeLINK take
AdjustModifiedNucleotides into account too.


Regards,

ClAuS (for BUSTER Develpers)