Frances Bernstein writes: > In the PDB format document there is a new record type > specified that has not yet been implemented. It would seem > useful to have an equivalent in an mmCIF but I could not find > any in the dictionary. Here are the relevant parts of the PDB > decsription: > > CAVEAT warns of severe errors in an entry. Use caution when > working with this entry. > > COLUMNS DATA TYPE FIELD DEFINITION > 1 - 6 Record name "CAVEAT" > 9 - 10 Continuation continuation Allows concatenation of > multiple records > 12 - 15 IDcode idCode PDB ID code of this entry > 20 - 70 String comment Free text giving the > reason for the CAVEAT > > PDB will add this record to incorrect entries that are not withdrawn > from the set of released entries. This record will be used sparingly, > and only after an external review has been made. > > CAVEAT will be added by the PDB to entries known to be incorrect. > > Example: > > 1 2 3 4 5 6 7 > 1234567890123456789012345678901234567890123456789012345678901234567890 > CAVEAT 1ABC THE CRYSTAL TRANSFORMATION IS IN ERROR BUT IS > CAVEAT 2 1ABC UNCORRECTABLE AT THIS TIME Since this is a PDB specific issue, we decided to handle this by creating a category, DATABASE_PDB_CAVEAT. This is *almost* parallel to DATABASE_PDB_REMARK - the lack of parallelism is be illustrated by the examples. For DATABASE_PDB_REMARK, we have: ; loop_ _database_PDB_remark.id _database_PDB_remark.text 3 ; REMARK 3 5HVP REMARK 3 REFINEMENT. BY THE RESTRAINED LEAST-SQUARES PROCEDURE OF J. 5HVP REMARK 3 KONNERT AND W. HENDRICKSON (PROGRAM *PROLSQ*). THE R 5HVP ; 4 ; REMARK 4 5HVP REMARK 4 THE TWO CHAINS OF THE DIMERIC ENZYME HAS BEEN ASSIGNED THE 5HVP REMARK 4 THE CHAIN INDICATORS *A* AND *B*. 5HVP ; while for DATABASE_PDB_CAVEAT, we have loop_ _database_PDB_caveat.id _database_PDB_caveat.text 1 ; CAVEAT 1ABC THE CRYSTAL TRANSFORMATION IS IN ERROR BUT IS ; 2 ; CAVEAT 2 1ABC UNCORRECTABLE AT THIS TIME ; the distinction being that for REMARK the id is extracted from the PDB record, while for CAVEAT is is simply a running number made up to provide a label for each line. This could be changed if is was felt to be unncessarily clumsy - the alternative would be a making CAVEAT not a looped list, but a single data item into which all CAVEAT records were read. Fran may want to comment on or rewrite the definition for the category, which I have just made as boilerplate. ; Data items in the DATABASE_PDB_CAVEAT category record details about features of the data block flagged as 'caveats' by the Protein Data Bank (PDB). These data items are included only for consistency with PDB format files. They should appear in a data block only if that data block was created by reformatting a PDB format file. ; Paula ******************************************************************************** Dr. Paula M. D. Fitzgerald ______________ voice and FAX: (908) 594-5510 Merck Research Laboratories ______________ email: paula_fitzgerald@merck.com P.O. Box 2000, Ry50-105 ______________ or bean@merck.com Rahway, NJ 07065 USA (for express mail use 126 E. Lincoln Ave. instead of P. O. Box 2000) ********************************************************************************