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 can’t reproduce this (CCP4-6.1.13), but I’m immediately suspicious of the apostrophe (U+0027) character in the error message. I’m not a DNA dabbler, so I can’t 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, they’re primed I think. -- Best wishes, Ian.
