Andrew The default libraries installed at LMB are for the latest refmac/libcheck, which use PDB v3 names for nucleotides (ie with primes), for both refmac and coot
The older libraries are around somewhere I get extremely confused by this sort of thing Phil > Hi Ian, > > This is bizarre, we also have 6.1.13 installed here, but in my ADN.cif > (dated Oct 29 2008) the atom names have primes, but are surrounded by > quotes which I think allows a mechanism for them to be converted to a > * if you have the appropriate changes listed in your (personal) library. > > I don't understand why these differ (unless Phil change the ADN.cif > entry here for some reason). > > I think we need a comment for the library people ! > > Cheers > > Andrew > > > On 15 Mar 2011, at 14:23, Ian Clifton wrote: > >> On 15/03/11 12:57, A Leslie wrote: >> >>> >>> I then try using LIBCHECK standalone to get the PDB file. I get the >>> same error if I use the FILE_CIF input keyword and give it the >>> filename for ADN.cif, no surprise, as this is (I assume) what COOT >>> does. >>> >>> I then copy over ADN.cif to my local directory, run LIBCHECK again >>> and >>> use the FILE_L keyword to specify the (local) ADN.cif file. I then >>> get >>> the error: >>> >>> ERR: item _chem_comp_tree.atom_id :O2' not found in the atom list >>> MON,BLOCK :ADN data_comp_ADN >>> >>> suggesting that there is an error in ADN.cif ! >>> >> >> I cant reproduce this (CCP4-6.1.13), but Im immediately suspicious >> of >> the apostrophe (U+0027) character in the error message. Im not a DNA >> dabbler, so I cant help much, but I bet the problem is due to >> primed >> atom names being replaced by stars, or something else. In my CCP4 >> distribution, the atom names are starred in the dictionary file for >> ADN. >> In official PDB files, theyre primed I think. >> -- >> Best wishes, >> Ian. >
