Re: [ccp4bb]: Using new library in Refmac5

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

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Pavel Golubkov wrote:

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>
> I am having problems refining my ligand in Refmac5 in ccp4.1.1i. I have 3
> monomers and 3 CoA molecules in the pdb file. The monomers by themselves
> refined just fine, but I want to refine with the ligand. I don't want to use
> the refmac5 library for CoA, so I created my own from pdb using Sketcher. My
> question is, which library do I give refmac for LIB_IN? I am still refining
> protein, so I need mon_lib_prot.cif, but I don't want refmac to use its own
> CoA library in mon_lib_1.cif and instead use COA_mon_lib.cif that came out
> of Sketcher. I tried specifying this library when setting up refmac, but I

If you give LIBIN and some of monomer names coincide with  library then program

will take your monomer description. Reason for WARNING and creating new
dictionary could
be that your coordinates may not be ideal. To force program use dictionary
description without checkong
validity you can use

MAKE CHECK none

in the command line. Or using interface in the SETUP RESTRAINTS section you can
specify that do not check anything.
Then it should work o.k.

Garib

>
> get the error:
> Number of atoms    :    5238
>   Number of residues :     672
>   Number of chains   :       6
>   I am reading library. Please wait.
>                 mon_lib.cif
>   WARNING : COA      : program can not match library description....
>                           program will create new complete description
>   WARNING : COA      : default angle value will used
>                   chem_type : P   -O2  -C     120.000 (P3  -O3' -C3' )
>   WARNING : COA      : default angle value will used
>                   chem_type : C   -CT  -NR5   109.500 (C2' -C1' -N9  )
> .......... etc.
> Which to me looks like it doesn't know what COA is. By the way, this new
> library works, I tried loading it in Sketcher and it correctly lists COA as
> the only non-polymer ligand with correct geometry and atom names. I guess a
> more general question would be how to make refmac use its default library
> for peptide, but user-specified library for ligand? Any help would be
> greatly appreciated.
>
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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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