Mutation annotations about icn3d HOT 6 CLOSED

That's a great idea! I will add more text to label the wild type and mutant in the next release. To add a label, you can select one residue with residue ID as "resid" and show the label in the center of your selection using the following code:

let position = ic.applyCenterCls.centerAtoms(me.hashUtilsCls.hash2Atoms(ic.residues[resid], ic.atoms));
let x = position.center.x;
let y = position.center.y;
let z = position.center.z;
let size = 0;
let color = 0;
let background = 0;
ic.analysisCls.addLabel(text, x, y, z, size, color, background, 'custom');

from icn3d.

@msierk I released the update. Now you will see the label "Wild Type" and "Mutant":

from icn3d.

from icn3d.

Thanks, @jiywang3!

great. maybe default the size of sticks 0.3 or 0.2 ... it is a little too fat also ...

I agree, I've been setting the stick radius to 0.2 for 3DVizSNP

mutations may not necessarily be from wild type ... this is the majority but not a necessity here you assume the reference starting sequence is wild type just a note. It is not a big deal ...

Yes I've run into this issue with 3DVizSNP. I've been selecting the 'best' PDB structure from the PDBe REST API, but I found out with KRAS that it was picking a structure with an engineered mutant at the site I was looking at, so there was a mismatch between what you see in the scap command and the 3DVizSNP mutant, which is based on the Uniprot sequence. I'm working on implementing a check for this. There is another API call that can tell you if there is an engineered mutant, but it would be nice if PDB had a more straighforward way to label things as wt or not.

from icn3d.

@jiywang3 I see the labels in the 2D panel, but my original comment was directed at the label in the upper left of the 3D panel. Would it be possible to change that?

from icn3d.

@msierk I added the text label in 3D display as well.

from icn3d.