mdsrv
under macos with apache, will ask when I have a more specific problem.
MDbox
looks very promising but there's no continuation of it now https://conference.eresearch.edu.au/wp-content/uploads/2017/07/Karmen-Condic-Jurkic.pdf
AllChem.AssignBondOrdersFromTemplate
)
Hi all, long time no see / write :)
Has anyone @fredludlow for instance integrated something in the NGL codebase to correctly parse MMCIF bond orders for HETATM's not from the external components cif, but from a loop section like this as supported by the standard itself:
loop_
_chem_comp_bond.comp_id
_chem_comp_bond.atom_id_1
_chem_comp_bond.atom_id_2
_chem_comp_bond.value_order
_chem_comp_bond.pdbx_aromatic_flag
_chem_comp_bond.pdbx_stereo_config
_chem_comp_bond.pdbx_ordinal
5CV C32 N29 SING N N 1
5CV C32 C33 SING N N 2
5CV C38 C33 DOUB Y N 3
...
Whats the easiest way to superpose all models within one structure?
I was hoping I could do something like this:
var s = r.structure
NGL.superpose(s, s, true, "/4", "/0")
NGL.superpose(s, s, true, "/3", "/0")
NGL.superpose(s, s, true, "/2", "/0")
NGL.superpose(s, s, true, "/1", "/0")
r.updateRepresentations({ position: true })
r.autoView()
But that doesn't work.
var s = r.structure
var base = s.getView(new NGL.Selection("/0 and .CA"))
for (var i = 1; i <= r.structure.modelStore.count; i++) {
var view = s.getView(new NGL.Selection(`/${i-1} and .CA`))
var superposition = new NGL.Superposition(view, base)
superposition.transform(view);
}
r.autoView()