On 30/01/15 18:14, Murpholino Peligro wrote:
> hello everybody!
Hello Murpholino Peligro,
> I was just getting a better structure from the 193L.pdb with coot
> (Fetch PDB and map using EDS) Everything was ok,...but the last
> residue (129) could not be refined ...The warning that appeared was
> something like ->
>
> INFO:: check_dictionary_for_residues - problem...
> WARNING:: Failed to find restraints for :CL:
When I read in the PDB file, I see:
INFO:: using standard CCP4 Refmac dictionary to search for "CL"
There are 2 data in /extra/paul/ccp4/ccp4-6.4.0/lib/data/monomers/c/CL.cif
INFO:: using standard CCP4 Refmac dictionary to search for "NA"
There are 2 data in /extra/paul/ccp4/ccp4-6.4.0/lib/data/monomers/n/NA.cif
INFO:: making map from mtz filename coot-download/193l_sigmaa.mtz
You see that coot finds the CL restraints in the same place that it
finds the others (standard amino acids). I wonder why that appears not
to be the case for you.
>
> Strange thing was that in only occurs with the last residue.
Yes. Residue 129 is a LEU. Residue 130 is a CL. I didn't have any
problem refining residues 129 or 130.
> I try to change the pdb Chloride atom to CL- but didn’t work ..
No, in fact I don't know how you'd do such a thing.
> I have ubuntu 14.04+openbox and coot's official build for that platform.
Good for you. Please do a
$ coot --version-full
for me please.
Paul.
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