Re: [ccp4bb]: cif files of unknown ligands

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

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On Monday 05 Aug 2002 4:31 am, sameeta bilgrami wrote:
Dear Sameeta,

If you want to use links they should also be described in the dictionary. 
Links are like residues can have bond, angles, planarity etc.

Refmac tries to match you coordinates with dictionary description. When 
coordinates are not good enough then it may fail to find match. To force it 
to use current description without checking you need to use
make check none (or in ccp4i Do not check anything)

then program will rly solely on your naming convention.

And program may give lots of warnings and info about close contacts. They are
worth to look at but may be ignored.

Reagards
Garib

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> ***          CCP4 home page http://www.ccp4.ac.uk         ***
>
> dear all,
>      hello,
> i have a ligand in my protein structure which i am
> trying to refine... i made the cif file using sketcher
> ......but refmac does not seem to run ...however if i
> put the ligand far enough from the protein molecule
> (without it having any contacts), refmac does not seem
> to have any problems...i tried including the link
> statement in header of the pdb file but that also did
> not work....there is also a cif file made by refmac
> itself ...if i use that file the program seems to run
> but the geometry of the protein becomes bad and so
> does the density....i compared the cif file made by
> the sketcher and that made by refmac ...the one made
> by refmac seems also to have link information in it
> ..... so how do we include the correct link information
> in the cif file ...is there a way to do it by means of
> monomer library sketcher ....thanx in advance for the help...sameeta
>
> =====
> Sameeta Bilgrami
> Research Scolar
> Deptt. of biophysics
> All India Instt. of Medical Scs.
> India
>
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-- 
Garib N. Murshudov, Chemistr Department, University of York
Tel: (01904) 328252