Electron Density Discussion

Started by inkycatz

alcor29 Lv 1

I like EDs. They take a lot of work however. If a lot more time were allotted, in addition to all the improvements mentioned above, perhaps more people would try to work on them

alcor29 Lv 1

I think that should be polled or discussed with the general membership. (I myself can't do EDs anymore due to physical limitation.)

inkycatz Lv 1

That of course, is always a good idea, however as you did bring up the idea, you clearly have some preferences!

It's cool to have opinions! That's what the thread is for.

alcor29 Lv 1

Well, I have no preference since I can't do them at all any more due to an arm difficulty no matter how much time I had. So I guess I'll withdraw the suggestion. My apologies.

alcor29 Lv 1

I hadn't seen Susume's answer. Her specs seem like an improvement which might invite more appreciation and participation.

tokens Lv 1

It was really nice to see puzzle 1287. However I would also like to see small denovos with an ED cloud to make the task a bit more difficult while still being easier than the "real" ED puzzles.

Bruno Kestemont Lv 1

-revisiting almost solved puzzles: 7 days
-easy short puzzles: 10 days

-flat heavy de novo: 30-40 days

Background: We needed the all 45 days to build the puzzle of the paper.

First you must find some free time to start the puzzle (several hours are needed to explore the density). This could make you wait a couple of days before starting playing.

Then you spent >1 hour to find the tryptophans or other starting point inside of the cloud and on the puzzle. Your time is over for next day.

Then another day, you start walking in the cloud. This is extremely slow (at least on my computer) when the cloud is visible on screen. One hour a day, 15 hours needed for me = 15 days.

Then you refine the all structure.

Total 20 days to finish the full hand design

Then you can start to share to team and to use recipes. Cloud view disabled to save time.

But some time, you have to manually correct your density (and find the 1 free hour for it). Total + 10 days = 30.

If there are disordered loops, add 10 days.

Total 30-40.

alwen Lv 1

One thing I noticed while working on 1287 is how much changing a sidechain's position (rotamer) can affect the fit to density.

We could use some better tools for changing rotamers, other than scripts. As far as I know, the only way to change rotamers without a script is the < (left arrow) in Selection Interface, and sometimes this is crashy.

Pulling on a sidechain changes the rotamer, but not with any sort of control.

I got some pretty good jumps running scripts like Rav Snap and Wiggle, and using the spacebar to make it skip positions that obviously didn't fit the density.