Paul Emsley wrote:
Les Tari wrote:
I realize that I left out a key detail, and had a typo on my last post. I am running Coot 0.5 on OSX (intel). The error message I see when I try to refine a monomer I generate with the CCP4 monomer library sketcher that there are NO restraints found for the ligand (despite the fact that I read in the mon_lib.cif file before reading in the coordinates for the monomer(s) in question).

Les,

When one successfully reads a dictionary cif file (typically monomer-XXX.cif, if it has come from LIBCHECK via Coot) Coot will tell you that it has read n bonds from the dictionary - if it doesn't do that then I worry. Look for "dirty cif?" message in the console.

Are you sure that the three-letter-codes of the PDB coordintes match that in the cif dictionary?

How, more precisely, did you make you dictionary? I presume this is a ligand you designed yourself (and not something in the refmac dictionary?).

For the archive:

This was resolved off-air. The PDB file out of sketcher had 2-char atom names formatted like this: "C2 ", whereas Coot (which tries to match dictionary atom names with PDB atom names) expects 2-char atom names to be formatted like this: " C2 ". An alternative solution (not tested) would be to quote the atom names in the dictionary cif file.


Paul.

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