[Xplor-nih] Metal-cluster

[Hongyan Li]

Dear Charles,
Thanks for your advice. I don't know how to vary Cd-S distances and angles when
generating PSF file. Any suggestions?
Best wishes,
Hongyan

Quoting Charles at Schwieters.org:

> -----BEGIN PGP SIGNED MESSAGE-----
> Hash: SHA1
> 
> 
> Hello Hongyan--
> 
> > I used formatconverter to convert NOE format from Cyana to CNS, it works
> fine
> > for my other protein without metal ions. I still believe that something
> wrong
> > with PSF file. Since in the metal cluster, Cd-S distances and angles were
> > fixed, but in this protein, for each Cd, both Cd-S distances and
> > angles varied according to our Cyana structures and published structures.
> > 
> 
> you might do a survey of the pdb to find the observed range of these
> bond lengths and angles. You are correct that you should allow the values
> to vary in this structure if they are not found to be constant.
> 
> > I got Cd radius of gyration value from parameter files of CNS
> > (ion.param), not sure where to get proper value.
> 
> if the selection you specify in initCollapse is globular (it should be),
> then the default Rg it calculates should be reasonable.
> 
> best regards--
> Charles
> -----BEGIN PGP SIGNATURE-----
> Version: GnuPG v1.4.6 (GNU/Linux)
> Comment: Processed by Mailcrypt 3.5.8 <http://mailcrypt.sourceforge.net/>
> 
> iD8DBQFGI4SLPK2zrJwS/lYRAo3BAJ9WiBJ6uwiZGKjo4LAuwASxAOT/XACfennz
> MKp4ugdoKf6bvvEKMimAFbA=
> =mbu0
> -----END PGP SIGNATURE-----
>