[buster-discuss] Big trouble with MLY

[Kikuti Carlos]

Hey Phil and Rohan,

Thank you for your replies. I have only 2 copies of MLY.cif in the computer, one is in $CCP4/lib/data/monomers/m, the other one is in Coot’s directory under $CCP4, and they are identical. So I guess Buster is taking the one from $CCP4, right?

If that’s correct, then yes, it is already as peptide:
MLY MLY N-DIMETHYL-LYSINE peptide 30 12 .


  *   Which is curious because, also for M3L for which the TER line is not added, Buster will always convert them to HETATM, even if you manually edit the pdb file.

In Coot, the peptide bonds around the newly added MLY look OK, but I created the LINKs as suggested by Rohan anyways:
LINK         N   MLY A 189                 C   THR A 188     1555   1555
LINK         C   MLY A 189                 N   LYS A 190     1555   1555

But when Buster takes it up, it is still creating the TER line at aa 188… Even if I tell it Pdb2Tnt_RunAdjustLNNN=yes

I believe this is something within the Buster/TNT/Gelly code, but my skills are not that developed to find where exactly… I wish there was a keyword like CreateTERLineBeforeSpecialResidue=no …

Anyways, for the moment I using a workaround that I’m describing for records, for when other people face the same issue:

  1.  Modify the refine.pdb: remove the TER line before the special amino acid;
  2.  Convert it to mmcif (for instance with https://mmcif.pdbj.org/converter/ );
  3.  Download the resulting mmcif file and submit that to Validate.

This is much easier (at least to me) than modifying directly the BUSTER_model.cif, which requires many more changes (all those exclamation marks).

Well, I’m still on the lookout for a real solution.

All the best,

---------------------------------------------------
Carlos KIKUTI, PhD
UMR144 - CNRS - Institut Curie
Pavillon Trouillet Rossignol
26 Rue d’Ulm - 75005 Paris, France
carlos.kikuti at curie.fr<mailto:carlos.kikuti at curie.fr>

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