Re: [ccp4bb]: ncs in refmac5

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

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Hi 
Zn as element in the dictionary. If you want to add links then you can run 
refmac5 with 
make link yes 

then program will write all possible links to your pdb file and will create 
cif file. Then you can edit and use these links for restraints. 

With NCS problem. If you are using sgi and ccp4 4.2 could you please try 
refmac from york's ftp site
ftp://ftp.ysbl.york.ac.uk/pub/garib/

There is slight problem with refmac5 on sgi in ccp4 4.2. It is being dealt 
with.

Regards
GArib

On Wednesday 10 Jul 2002 5:08 pm, Thomas Scott Reid wrote:
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>
>
> Thanks for earlier advice on how to apply TLS parameters to my protein,
> which has lowered both the R and Rfree by 1 and 2%, respectively.  I've
> got six molecules in my asymmetric unit (one TLS per molecule), and now I
> want to move on to applying both NCS restraints (which I've found, at
> least in CNS, to greatly improve stereochemistry and lower the Rfree)
> along with TLS restraints.  Unfortunately, I've hit a wall.
>
> The problem is everytime I include NCS restraints, the program chokes and
> gives me a 'problem with NCS' message.  However, I've found that this
> problem is eliminated by getting rid of the catalytic zinc ion in my pdb
> file.  Therefore, I don't think there is anything wrong with the NCS
> syntax - rather, there is some other problem lurking in the shadows. Any
> explanation for this phenomenon would be greatly appreciated.
>
> Because my pdb is coming straight out of CNS, which I've been using for
> some time, there must be something I'm missing in my library file.  I'm
> simply letting Refmac5 read in the old CNS pdb file and then create the
> appropriate .cif file.  Specifically, do I need a special library file to
> describe the Zn+2 ion and its coordination sphere?  The zn ligands are
> unusual - an Asp(2 bonds), Cys and His (1 bond) and a substrate ligand,
> which can have either a sulfur or a nitrogen.  The zn appears in the pdb
> file as follows:
>
> ATOM   5423 ZN+2 ZN2 Z   1      26.149  91.599  68.426  1.00 45.67      Z
>
> I have tried other notations for the Zn in the pdb file (taken from
> deposited pdb files), but to no avail.
>
> Also, does anyone know of any programs that can create
> rendered/anti-aliased figures that show the Richardson's contact dots?
> Xfit, although it displays them, doesn't seem to send them to Raster3D for
> rendering.
>
> All suggestions are appreciated.  Cheers.
>
> T. Scott Reid
> Duke Univ. Med. Center
> tsr@duke.edu

-- 
Garib N. Murshudov, Chemistr Department, University of York
Tel: (01904) 432565