Looking at the code (!) here are the rules for those statistics.
It excludes elements that are not in (H, C, N, P, F). So it excludes O.
It excludes water exchangeable atoms. So it excludes HG1.
Backbone is (H, N, C, CA) so excludes HA (so that is "side chain").
Amide is (H, N) (as you have below).
It only includes one atom per atomSet, so HG2* counts as 1 (as you have below).
Yes, some semi-arbitrary rules there.
On 3 Jul 2014, at 09:39, Justin Lecher wrote:
> Hi everyone,
> I am sitting here and try to figure out how the atom counting in the
> "Atom Assign Status" works.
> For simplicity I took a central Thr which is protonated at Hg1
> Assigned atoms are HN, HA, HB, HG1, HG2*, N, C, CA, CB, CG2
> The dialogue tells me the following
> Category Available Assigned
> Element C 4 4
> Element H 4 4
> Element N 1 1
> Amide 2 2
> Backbone 4 4
> Backbone non-H 3 3
> Side Chain H 3 3
> Side Chain non-H 2 2
> Type N 1 1
> Type H 1 1
> Type HA 1 1
> Type HB 1 1
> Type HG 1 1
> Type C 1 1
> Type CA 1 1
> Type CB 1 1
> Type CG 1 1
> My question is what are Amide, Backbone and so on?
> This is what I guess:
> Amide HN + N
> Backbone HA, CA, C, O
> Backbone non-H CA, C, O
> Side Chain H HB, HG1, HG2*
> Side Chain non-H CB, CG
> So here are some points which make me wonder:
> * Summing up all H (HN, HA, HB, HG1, HG2*) is 5, but "Element H" says 4.
> * Why are "Amide"s not counted in the backbone.
> * "Type HG" says 1 although the molecule definition has 2 HG (HG1, HG2*)
> and we assigned the HG1.
> Could some please help me to understand this?
> Justin Lecher
> Institute of Complex Systems
> ICS-6 Structural Biochemistry
> Research Centre Juelich
> 52425 Juelich, Germany
> phone: +49 2461 61 2117