Re: [Jmol-developers] Re: secondary structure

[Miguel <mi...@jm...>]

Andreas wrote:

> browsed up the code to the point to where Helices are calculated and
> HBond partner - offsets are stored in mainchainHbondOffsets=5B=5D.
>
> Offsets are required to determine Helices. For sheets it is needed to
> store all HBonds in another array. Additionally,  each amino
> acid can be donor or acceptor of two H-bonds. DSSP calls this
> =22bifurcated=22 H-bonds. Basically energyMin1, indexMin1 and
> energyMin2,indexMin2 in bondAminoHydrogen should be stored and are
> needed for method =22bond=22 in the pseudocode below.

I have checked in code which mimics this.

For each donor residue the energy values and indexes of the acceptor are
saved.

> pseudocode to calc sheet H-Bond pattern:
> for a in aminos:
>   for b in aminos:
>     // testing for parallel :
>     if  ( bond(a+1,b) && bond(b,a-1)) =7C=7C
>         ( bond(b+1,a) && bond(a,b-1))
>     found parralel bridge
>
>     // testing for antiparallel :
>     if ( bond(a,b)     && bond(b,a)) =7C=7C
>        ( bond(a+1,b-1) && bond(b+1,a-1)
>      found antiparallel bridge.
>
> and the code for bond:
>
> boolean bond (i,j)
>     if ( ( i.acceptor1.index =3D j && i.acceptor1.energy < cutoff )=7C=7C=

>          ( i.acceptor2.index =3D j && i.acceptor2.energy < cutoff ))
>             return true ;
>     else return false,

Once I find these bridges, it is not clear to me which residues should be=

tagged. At first I thought that only the donors should be tagged as
'participating in a sheet'. But then I decided that we needed to tag the
recipients as well.

> according to the code in AminoPolymer =22cutoff=22 could be -500 which =
is
> also the cutoff used during the calculation of the energy.

OK

> then we have got the basic elements of sheets: H-Bond bridges.
> Several bridges are connected to a sheet if they involve consecutive
> residues.

In using 1CRN.pdb none of the bridges are consecutive (unless I tag both
the donors and recipients). Even then, there are things that look like to=

me that they should be tagged, because their two neighboring residues are=

participating in the sheet.

But, if I allow gaps in the tags then non-sheet things get included.

Please advise


Miguel


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