[Date Prev][Date Next][Thread Prev][Thread Next][Date Index][Thread Index]

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

***  For details on how to be removed from this list visit the  ***
***    CCP4 home page http://www.dl.ac.uk/CCP/CCP4/main.html    ***

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?


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