Good day all,
In COOT, when I view my coordinate pdb file with my
ccp4 map file (using "Auto-open mtz"), I have a couple
residues for which only a part of the peptide chain is
visible. E.g. for a Lys, only the terminal nitrogens
at the end of the R-group chain are visible as bonds.
The other parts of the residue (and even parts of
adjacent residues) are visible only as stars/stellate
points that may or may not be within my blue electron
density. If I click on the stars, the atom names that
appear are consistent with the missing peptide chain,
and correspond to the "missing" amino acid that has
the occassional visible R group.
Just wondering what this means, that I am seeing
stellate points that seem to be acting as place
holders for my residues in a couple locations in my
structure. The structure was obtained using molrep.
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