Centroid devprev test puzzle bugs

Started by Bletchley Park

Bletchley Park Lv 1

  • It is said that sidechains are represented by a single large atom, they are not.
  • Sidechains should have only one position and shake should have no effect, sidechains are normal and can move around as they always do, shake massively improves score.

This thus defeats the purpose of the puzzle.

tamirh Lv 1

Sorry, the centroid mode wasn't actually enabled on that devprev puzzle. I believe jflat06 puzled the puzzle out from devprev for now.

We'll post a centroid puzzle once the new devprev client goes out.

Centroid mode is activated per-puzzle. Instead of calculating all of the atoms of the sidechains, it estimates them as single values. You will notice sidechains are all rendered as spheres of varying sizes, so it should be pretty apparent when it's actually enabled.

marie_s Lv 1

On the graphical proposition : I don't know how you can fold without seeing the AA.
The classical view have to be accessible even with no possibilities to shake the sidechains.

on wiggle sidechains : this tool is modified or not?

on wiggle : wiggle froze almost every timeeven with ci = 0

wiggle with bands move very quickly

Susume Lv 1

If you click "Show expected residue burials" in the centroid puzzle, the client crashes. Latest devprev, Win 7 64.

end of Log.txt:

ERROR: AtomTypeSet: unrecognized atom parameter: SASA_RADIUS
ERROR:: Exit from: E:\vmuser\foldit\mini-interactive-main-release\rosetta_source\src\core/chemical/AtomTypeSet.hh line: 142
ERROR: Rosetta exit unexpectedly
SRVR_THRD getting notifications…

tamirh Lv 1

Thanks for testing the puzzle out.

The atoms of the AA are only roughly approximated in centroid mode which speeds up the scoring of the protein. Because of this, there is no absolute position information for all of the atoms of the amino acids. Drawing them in any particular way would be misrepresentative. Because of this, they are just drawn as spheres, as that's basically how they are being approximated in centroid mode.

I will check with some people, I believe wiggle sidechains doesn't do anything in centroid mode. I'll get back to you on this though.

For wiggle freezing up, could you share a solution with yourself with the protein in that configuration and tell us the name? It's much easier for us to look into it with the exact pose.

tamirh Lv 1

Thanks for catching that. I think 'show expected residue burials' is expecting some information that is not available in centroid mode. I'll fix that.

marie_s Lv 1

wiggle problem : testwigglecentroid

Information on segments are on tab, I want to see this information to fold the protein because I choose the shape of the protein with this information: not all segments are in corner, not all hydrophobes are outside…