Hi,
I wanted to create a restraint file for CNS from Analysis and I had a couple
of problems:
I imported a spectrum and I started to assign the crosspeaks. However,
I didn't get why the streospecific protons have the numbers 2 and 3 (i.e.
HB2 and HB3). Going to CNS latter on, it is not consistent with the name
given by CNS (HB2 and HB1 are defined in the topology file of CNS for every
amino acid). Also the HN proton (called HN in CNS) is called H in
analysis... Is there any reason for this?
Then, I tried to export the crosspeaks in a the "ARIA format", I realised
that things are different from the output produced by "connect" in AZARA.
-The atom names differ from the names given by CNS (as I said above).
-The distances d, dminus and dplus used in the aria-list is also different
(i.e , with azara we get 5.0 5.0 0.0 ; with analysis 5.0 0.0 5.0). Clearly,
dminus and dplus are swapped. I'm confused because CNS gives the following
syntax :
assign <atom-selection> <atom-selection> <real> <real> <real>
1st-set 2nd-set distance dminus dplus.
But it seems that dminus should be the highest distance (5.0 in my example).
Finally, a pratical question about how to choose the size of the box when
you want to calculate the volume of your crosspeaks?
cheers,
Marc
|