Hello Silvia--
> There are 2 parts to this question.
> 1.Background is: we have managed to make the default scripts run and
> create the right thioether linkages and Dha/Dhb residues, but we
> have two peptides of 28 and 20 aa that have lysine sidechain protons
> all the way up to 0.9 and 0.99 ppm-referenced to DSS (and there are
> aromatic residues in the peptide as well). This is highly suggestive
> that the lysine HD/HG should stack on an aromatic sidechain, right?
> in at least one of the structures, the Lys sidechain could easily be
> rotated to come in proximity with the aromatic ring but the
> calculation results don't place it there, there are NOEs to support
> this, but the calculations don't favor it, in fact such a structure
> is nowhere in the lowest 20/100. How do I implement this?
You might try ambiguous distance restraints for this: one restraint
might be between any LYS NZ/aromatic group using ASSIgn ... OR
distance restraint statements. Perhaps you want to try a restraint for
each LYS.
>
> 2. I've tried mimicking the csPotTools.p y script, but the
> calculation won't run at all saying "cannot convert 4 letter residue
> to 3 letter" (because we defined cyclized aminobutyrine/alanine as
> D-Abu or Abu or D-Ala, ALA depending on the stereochemistry-see
> below). I have a feeling even if they were defined as 3 letter,
> camShift or whatever it is that does this wouldn't recognize them. I
> apologize if I don't know some of the inner workings I should, but I
> can't find a comprehensive explanation on how to do this anywhere.
> See below for the specific error:
>
> k=create_CSPot("ProcA21_csPot.tbl",cs )
>
> Error converting String DABU into amino acid index: not a valid
> 3-letter code
The chemical shift predictors won't work so well for unusual amino
acids, so they should be omitted. Please see if this works:
k=create_CSPot("ProcA21_csPot.tbl",cs,
selection="not (PSEUDO or resname DABU)")
Let's see how these ideas work, and go from there.
Charles
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