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.
