I know you've shared solutions for this crash on previous puzzles—if you also have a solution that crashes reproducibly on this puzzle and can Share with Scientists, that would be still helpful.
Or does Foldit crash when wiggling the start structure, immediately after opening the puzzle?
It will crash when wiggling the start structure, immediately after opening the puzzle. Let me know if I can provide any more information.
Just for (fun) reference, can you give us the resolution of the ED?
This map has a resolution limit of 1.20 angstroms.
Thanks. The number is a bit surprising to me if I compare that with the resolution of the previous puzzle 1357 at 1.5A. Puzzle 1384 has quite a few stretches of the protein that don't show up at all. I guess it makes sense if it is the maximum resolution this number is referring to...
So, if I read in a paper "the structure of protein x has been determined at 1.5A resolution" what does that mean exactly? On average 1.5A? Maximum of 1.5A? 1.5A except in variable regions? I know it is probably a bit pedantic, I just haven't thought about this much before Foldit ED puzzles.
Good question! When we talk about resolution limits in x-ray crystallography, we're talking specifically about the extent of x-ray diffraction (see the blog for more on diffraction). With respect to the electron density map, the resolution limit is just that—a limit. A resolution limit of 1.5 Å means roughly that the raw data contain no information about positions closer than 1.5 Å.
Other effects can "blur" portions of the refined electron density map—mostly having to do with ambiguous atom placement (e.g. thermal motion, partial occupancy, disordered regions).
resolution of this puzzle appears lower than others to me.
i hardly recognize few residue.
It has been already trimmed?
It seems odd to see a cloud with very clear outlines for interior atoms and no cloud whatsoever for whole residues (not just sidechains) at the protein surface. I can imagine the many long blue sidechains on the surface of a foldit design being floppy and maybe not having cloud, but I would not expect the very short loops in this protein to be disordered, would you? The complete lack of cloud for a tyrosine is also surprising. What is going on?
Another note - moving the threshold slider to the left usually shows more and more cloud, but in this puzzle a threshold of 0 shows the same as having it at a quarter of the slider - it's like the less-certain part of the cloud has been completely omitted.
Hmm, that's strange. In the full electron density map, all of the residues (and most of the sidechains) are well resolved. Something must have happened when we trimmed the density map for the Foldit puzzle. I'm sorry we didn't catch that before posting the puzzle!
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Density puzzles still crashing on linux.
20170503-ce4d057080-linux_x64
https://fold.it/portal/node/2003463
https://fold.it/portal/node/2002859