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[ccp4bb]: Re: protin.dict files with automated ARP scripts



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Couple of points:

The latest released protin.dic will work with SeMet.
Actually, the Met residue has been expanded to do both, you
simply select which atoms you want as appropriate. I've
written about this before - ask if you want to hear again.

Yes, we all hate protin. The good news is that the upcoming
REFMAC 5 won't use it. The bad news is that that means we're
not too keen to sit down and re-write the protin documentation.
There are several sections to protin.dic which need to be
edited. It is all explained at the end of protin.html but
it ain't pretty ....

Martyn

> 
> I'd like to follow up on this discussion in the arp-users list (also
> relevant for CCP4 I think:
> > 
> > Tommi Kajander wrote:
> > 
> > > I would like to know how to use self-made protin dictionaries
> > > for special amino acids like SeMet adn Cis-Pro with ARP
> > > ( i am new to using both protin and ARP)
> > > -where shoudl i have the protin dict-fiels for the special
> > > compounds for ARP to be able to read them???
> 
> Tassos Perrakis wrote:
> 
> > You will have to change the $warpbin/arp_protin.dic
> > file. for what it is and what you have to do, read first the
> > CCP4 documentation. Please ADD thing sin this dictionary,
> > do NOT susbtitute it, sicne it has a special definition for
> > waters which allows them to behave as 'freee atoms' when needed
> > during autobuilding.
> > 
> 
> I have modified protin.dic once to include info for glycerol, but the
> documentation is not completely clear on this. Apparently there are
> separate tables for bonds, angles, torsion, angles chiral centres etc
> but these are not labeled as such. I also missed these labels in the
> MAKEDICT output, so it took some fiddling to get it all right. Have I
> missed something or could this documentation be improved?
> 
> Flip
> 
> -- 
> P.J. Hoedemaeker Ph.D.
> Leiden Institute of Chemistry, Gorlaeus Laboratories.
> Einsteinweg 55 / P.O. Box 9502 2300 RA, Leiden The Netherlands.
> Department:     BFSC              Phone:      +31 71 5274211
> HTTP://wwwchem.leidenuniv.nl/bfsc	      +31 71 5274537
> ---------------------------------------------------------------
> "Nothing shocks me, I'm a scientist"		Indiana Jones
> 


-- 


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*                                                                        *
*                  Dr. Martyn Winn                                       *
*                                                                        *
*      Daresbury Laboratory, Daresbury, Warrington, WA4 4AD, ENGLAND     *
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