It seems that there is a mismatch between dictionary and libcheck versions. Could you please check 1) library vi $CLIBD_MON/a/ADN.cif
It should have primes like: ADN "O2'" O OH1 0.000 0.000 0.000 0.000 ADN "HO2'" H H 0.000 0.731 -0.600 -0.203 ADN "C2'" C CH1 0.000 -1.179 -0.442 -0.676 ADN "H2'" H H 0.000 -1.460 -1.449 -0.340 2) library version: vi $CLIBD_MON/list/mon_lib_list.cif the version should be something more than 5.23 (I think) 3) libcheck version libcheck the version should be something more than 5.1 If one of these is different then there will be inconsistency and most probably failure. I thought new version of ccp4 has all the latest versions. I may be wrong. regards Garib P.S. When you run libcheck it prints out the versions of the program and the dictionary. On 15 Mar 2011, at 14:43, Phil Evans wrote: > 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 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. >>
