[ccp4bb]: Difficulties with refmac5 dictionary usage: Problem #1

[Ethan Merritt <merritt@u.washington.edu>]

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Hi all:

I am having many problems in trying to describe new ligands for use in refmac5 refinement.
Here is one relatively simple one for which I hope someone knows a workaround.

By default refmac5 looks in $CLIB/data/monomers/  for monomer libraries.
If I define a new monomer and place in it a private library, I can have refmac5 look here
first by adding   LIBIN  ./private_mon_lib.cif    to the command line.
The problem is that if refmac5 finds some monomer in the standard libraries that
looks vaguely similar to mine, it insists on using that one instead of the one I explicitly
specified.  Is there some way to tell it _not_ to second guess my choice of descriptions?

quick description
-----------------------------

Here is a partial listing of the output file:
	Dictionary files for restraints : /usr/local/CCP4/asterix/lib/data/monomers/mon*cif
	Parameters for new entry and VDW: /usr/local/CCP4/asterix/lib/data/monomers/ener_lib.cif
	User supplied dictionary entries: ligands/private_mon_lib.cif
	[snip]
  I am reading library. Please wait.
                mon_lib.cif
  WARNING : monomer looks like ASO     program will use this one
  WARNING : monomer has the minimal description
                          program will create complete description

And then it complains that the geometry is horrible and it is defining a new ligand library f
or me to check and then it exits.

More details:
--------------------

I actually have ten copies of  the ligand in my structure.  It is quite large,
and I have not built the entire ligand into all ten sites.  With a great deal of struggle
I have managed to create a monomer library description for the entire ligand that
refmac5 accepts, and if the entire ligand is present it will use my library description
for it.  The problem comes at the sites where some atoms are missing.  Instead of
simply accepting it a partial fragment of the ligand type I specificy, refmac5 goes
and hunts in the standard libraries for some other ligand type with the same 
number of atoms, as shown above.

-- 
Ethan A Merritt       merritt@u.washington.edu
Biomolecular Structure Center Box 357742
University of Washington, Seattle, WA 98195
phone: (206)543-1421
FAX:   (206)685-7002