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Select residues - PDB structures


#1

Hi all!
Just downloaded and have been playing with Avogadro - great tool so far! If I may make a suggestion…I’m primarily interested in importing protein structures (fetching from PDB) and manipulating particular residues or sets of residues. Is there a way to select residues based on their location in the chain? For example, I might want to select residues that form the catalytic site (e.g. His57, Ser102, and Arg220), then display only those as van der waals spheres and the rest of the chain as ribbon. Or, to color those residues a bright color while the rest of the chain is dark grey. If there were a tool to custom select residues (maybe based on position in the chain, and ideally multiple residues at once) and style only the selected residues, that would be great! Additionally, omitting residues from a selection would be helpful (e.g. selecting the entire chain except for the above-mentioned residues).

One other minor issue I’ve come across…when using the pointer select tool to click on residues, the program consistently slows, freezes, and shuts down, but I don’t have the same issue when using the select dropdown menu.

Thanks! Keep up the good work!
-Sean


#2

Sounds like a great idea. (It’s fairly easy to invert a selection - so omitting shouldn’t be hard.)

I think the big question is how the UI would work… Can you sketch out or think about how the dialog would work? Right now, it’s pretty simple, just a name.

Would you add another line to optionally indicate the number? Or would you think the text box should interpret “His57” to be “select histidine, residue #57”?


#3

I think a text box that interprets user input (“His” to mean all residues, “His57” to pick a specific one at position 57, or maybe even just the position #) would make for an intuitive UI. This would also be nicely complemented with a hover feature, where hovering over a residue would result in a small pop-up box with the residue type and position displayed. I’m not much of a graphics programmer so I’m not sure how difficult these things are to implement…just passing along ideas for nice added features.

I’m also realizing that, with the structure that I’m interested, the ball-and-stick view seems to be primarily responsible for slowing/freezing. I can only rotate the molecule with a simpler view such as the ribbon view.

-Sean


#4

We’ve worked a lot to improve rendering performance in Avogadro 2, and it can handle millions of atoms. Unfortunately, it doesn’t yet have ribbons/cartoons or residue support. That’s next on the agenda.

Several people have talked about a hover feature, which seems like a nice idea to add to Avogadro 2. Suggestions on what should be included (e.g., if you’re over an atom, presumably, it would give something about the atom) are welcome in a new topic.


#5

As far as the selection, I think a “smart” parse of the residue name and number should be workable.