Mutation annotations

[msierk]

It would be nice to have a more descriptive label for the wt and mutant when looking at mutations. e.g. a _WT or _Mut instead of just a 2, which kind of blends in to the PDB or AF ID. I'm also wondering if the scap command could put a label on the mutated residue (e.g. A113S). I could try adding the label myself but I'd apparently need to know the xyz coordinates and I'm not sure how to get those.

add label ASN80 | x 7.082 y 15.36 z 9.254 | size 18 | color #ffff00 | background undefined | type custom

[jiywang3]

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');

[jiywang3]

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

[youkha]

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

…

On Sun, Apr 2, 2023 at 9:09 PM Jiyao Wang ***@***.***> wrote: @msierk <https://github.com/msierk> I released the update. Now you will see the label "Wild Type" and "Mutant": [image: image] <https://user-images.githubusercontent.com/11690222/229390344-939487d7-8190-4cbb-a3d3-1a0fb1441d46.png> — Reply to this email directly, view it on GitHub <#106 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/AD35NIMEMY2K3R5NUAJZ3MLW7IPNTANCNFSM6AAAAAAWLDU7LA> . You are receiving this because you are subscribed to this thread.Message ID: ***@***.***>

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[msierk]

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.

[msierk]

@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?

[jiywang3]

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