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

[Garib Murshudov <garib@ysbl.york.ac.uk>]

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Dear Ethan,

If you have have defined your ligand and have only part of that in your pdb (or your ligand in pdb
is not very good in terms
of geometry) then you can add

MAKE CHECk NONE ! do not check validity of ligands. Rely on users naming conventions (atoms and
residues)

then program will use your ligand description.

Regards

Garib

Ethan Merritt wrote:

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> ***          CCP4 home page http://www.ccp4.ac.uk         ***
>
> 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

--
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Garib N. Murshudov, Chemistry Department, University of York, U.K.
Tel: Home +44 (1904) 42 62 87, work:  +44 (1904) 43 25 65
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