"NUCLIN" sets up the stereochemical restraints for stereochemically restrained refinement of nucleic acids with the Hendrickson-Konnert method. The Hendrickson's refinement program for nucleic acids is "NUCLSQ".

NUCLIN is based on G. Quigley's "REFIN" (M.I.T.) and was extended by E. Westhof (IBMC-CNRS, 15, Rue R. Descartes, 67084 Strasbourg, France; BITNET : Westhof@FRIBCP51) for the incorporation of additional restraints and possibilities.

Present limit 5000 atoms and 30000 distances.

NUCLIN requires the following files :
NUCLIN.DC : (user transparent)
Dictionary of distances, angles, planes, and chiralities.
It is restricted to C(3')-endo sugars, but this can be corrected with IP=1 or IG=1 in NUCLIN.DAT on line 11.
DRUG.DC : user's own dictionary (N or #11)
RESTRAINT.DC : dictionary of weights and sigmas for restraints in NUCLSQ (written on LSQ.DAT if not present)
ABC.DAT : information on crystalline structure
NUCLIN.DAT : control cards.
HBND.DAT : list of H-bonds
ATOMS.DAT : list of atomic coordinates

NUCLIN outputs the following files :
NUCLIN.OUT : description of restraints
LSQ.INP : input for "NUCLSQ" (binary)
and either
LSQ.DAT : control cards for NUCLSQ (this file is produced only if not yet present)
or
LSQ.PAR : contains important parameters for LSQ.DAT (produced only if LSQ.DAT already present)

To run NUCLIN,
type NUCLIN Name-of-the-queue.
This assumes you have set the logicals with the SETHD.COM file.
Otherwise, you need in your LOGIN.COM : $ NUCLIN :== @Device:[.COM]SNUCLIN.COM
It is then enough to type :
NUCLIN Name-of-the-queue

The SNUCLIN.COM file contains :

$ ! SNUCLIN -- SUBMIT NUCLIN.COM WITH QUEUE SPEC.
$ bqueue = P1
$ if P1.eqs. "" then bqueue :="SYS$BATCH"
$ submit [.com]nuclin.com/queue='bqueue'/param=('f$directory()')
$ exit

The NUCLIN.COM file contains :

$ set default 'P1'
$ assign device:[.] NUCLIN_DIC
$ RUN [.]NUCLIN
$ EXIT

For reference, description and use, see :
Westhof, E., Dumas, P., & Moras, D. (1985) J.Molec.Biol. 184, 119-145.
Westhof, E., Dumas, P., & Moras, D. (1988) Acta Cryst. 44A, 112-123.