Output from "coot --version-full" 0.8.1 (revision 5478) [with guile 1.8.8 embedded] [with python 2.7.8 embedded] Binary type: Linux-x86_64-ubuntu-14.04-python-gtk2 Builder_info: build-host: ubuntu1404 on: Mon 05 Jan 1248.39 GMT 2015
Mr. Emsley and Mr. Caldwell have the dictionaries from ccp4i. I don’t have ccp4i installed on my lap, but on another machine. So I guess I should install the whole ccp4i suite (safer this way) or can I download the dictionaries from somewhere so coot can read them? 2015-01-30 13:16 GMT-06:00 Paul Emsley <pems...@mrc-lmb.cam.ac.uk>: > 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. > > >
