This thread is specifically for Susume's Electron Density Video. Thank you Susume!
Let's hear your questions about the video!
Thanks!
I still have no idea how random bits of blobby things in the bigger wooly blob can be identified as sheets. I think that whole process needs a LOT more explanation.
Now I'm impatiently waiting for the next video subsume introduced on the end of this one …
My main question would be for mid game: Now that I have many helices and loops in the cloud, how could I find the place for the sheets, since my all protein is interfering in my available views (slices etc). The method explained by subsume is good for start (even if you can misinterpret the big structures and start in a completely wrong direction - as I did :). How to use it at mid game?
Totally want to say THANKS Susume. I have been playing for about 2 years and I didn't even know you could add dots. Also I have other experiences navigating electron density in 'O' and COOT, which probably makes me different than most foldit players. I have been finding it frustrating to navigate density in foldit AND THIS VIDEO HELPED ALOT!
I want to beg Bitspawn to also do a video next! Is that possible? I have watched Bits dominate these kind of puzzles for a while now and would like some insight into the secret sauce.
This is really hard to express without an electron density cloud to refer to, but cloud sheets, just like in Cartoon view, will zig zag back and forth. Sidechains usually show as lumps on opposite sides.
This cloud has good resolution, so it is possible to identify some of the paddle (phenylalanine/tyrosine/tryptophan) sidechains.
If you look at a protein in Sphere view with sidechains showing, that is the one that most closely matches the cloud view, big and lumpy.
Hi
Could someone transcribe the video?
I do not understand a word O:-) and with the text I would like to put subtitles to this video.
Thanks :)
I don't know any way to get around the need for practice. Using the tools to narrow the field of view to a slice makes it possible to see shapes, but that by itself doesn't make them easy to identify. Hopefully seeing some samples and hearing some descriptions of the kinds of shapes to look for will help. Like any visual pattern, the first few are the hardest to see, and the more of them you see the more visible they will become.
The second video (on sidechains) also offers some views of a single sheet, with sidechains hanging off on either side. Maybe that view will be easier to recognize.
I have a transcript now for the first video, but I can't attach a file here in the forum. I will try to find a way to post it.
I had an option on the video viewer that automatically added a subtitle (I had no sound on this computer).
The English is quite aproximative but it was almost enough for me to understand what Susume explained.
There is even an option for translation but I did not try it (it would be worse than this automatic transcript).