How to draw a line connecting two residues?

[samuelflores]

Is there some trick that would enable me to draw a line between two nucleic acid residues, or for that matter two atoms ? Let's say I know the chain IDs, residue numbers, and atoms names, but not the atom indices. So I can't get the coordinates directly.

I am thinking maybe a Representation could be hacked for this purpose. How is the covalent bond network determined? Is it based only on distance, or does it come from the CONECT records? How about if I create a selection with just the two atoms, and then use e.g. Licorice rendering, and greatly increase the minimum covalent bond length, or in some other way specify that they are connected? Then the two atoms would appear to be bonded, and I would get the line I want. If that would work, kindly tell me how to do it.

[fredludlow]

Hi @samuelflores, does the solution in #924 help?

[samuelflores]

No, because I would have to know the coordinates. What I know are chain IDs and residue numbers. And atom names of course.

[fredludlow]

Covalent bonds are generated when the file is parsed, I don't think that's going to be an easy way to do it.

The reason I pointed at 924 was the example I'd posted there, copied here: you can go from chain, resno and atom name to selection, and the center of that selection is a coordinate (see how start and end variables are set) then build an arrow (or cylinder or whatever) using them.

stage.loadFile( "rcsb://1crn", { defaultRepresentation: true }).then(function (o) {
  stage.autoView()

  const start = o.structure.getView(new NGL.Selection("22:A.CA")).center
  const end = o.structure.getView(new NGL.Selection("33:A.CA")).center

  const shape = new NGL.Shape("shape")
  shape.addArrow(start, end, [1,0,0], 0.2)  // Or shape.addCylinder(start, end, color, radius)

  var shapeComp = stage.addComponentFromObject( shape );
  shapeComp.addRepresentation( "buffer" );
});

[samuelflores]

Oh this sounds like exactly what I want! However you seem to be using javascript or some such. How would I do this in python? I could find no documentation to help with that.

import nglview view = nglview.NGLWidget() view.clear_representations() pdbId = "1gid" view.add_pdbid(pdbId) for index, row in basePairingDataFrame.iterrows(): atom1String = str(row['nr1']) + "C1'" # here I am just creating an atom selection using residue number and atom name atom2String = str(row['nr2']) + "C1'" view.add_distance(atom_pair=[[atom1String, atom2String]], label_color="black", labelType = "text", labelText = "my text", color = "blue")

[fredludlow]

Ah, sorry, I see we were talking at cross purposes. @hainm: Given the JS recipe above is it possible to execute something like that through nglview?

Also, if you want to show base pairing the base representation type is available, e.g. https://codepen.io/fludlow/pen/bGLwJJM?editors=001&layout=left

[hainm]

Ah, sorry, I see we were talking at cross purposes. @hainm: Given the JS recipe above is it possible to execute something like that through nglview?

ah yeah, user can use view._execute_js_code (or just view._js): e.g: https://projects.volkamerlab.org/teachopencadd/talktorials/T017_advanced_nglview_usage.html