puzzle picture
1045: VipB Cryo-EM Density: Ghost Density
Status: Closed


201guygeva2311 79 1584  4,3121
202Primalsoul 77 200 Gargleblasters4,3021
203tck1988ca 79 1584  4,2991
204Talias 79 1584  4,2971
205NGanes 79 1584  4,2921
206bgiesy 79 1584  4,2871
207AryehK 79 1584  4,2641
208Paltiel 79 1584  4,2601
209perrya 79 1584  4,2581
210CaliberDied 79 1584  4,2441
211Ronin-Sensei 79 1584  4,2091
212mannre 79 1584 CHE 476 Advanced Biochemistry Laboratory University of Mount Union4,1371
213zaq1202 79 1584  4,0321
214roman madala 79 525  4,0291
215akii 79 1584  4,0231
216ktyk 79 1584  3,9931
217davidjakubec 79 1584  3,8731
218Otpk 79 1584  3,8351
219basakd 79 1584  3,7681
220EffJay 79 1584  3,6841
221guineapig 79 48  3,5731
222MadTrumpeter 79 1584  3,5541
223KarenCH 79 1584 Anthropic Dreams3,3861
224sushi810 79 1584  3,2061
225bataebi 79 1584  3,1111

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Joined: 10/30/2012
Groups: Beta Folders
without the density score the

without the density score the scripts are distorting the shape, for example the scorpion tail is getting pulled into the rest of the fold.

Batz's picture
User offline. Last seen 1 day 3 hours ago. Offline
Joined: 02/16/2012
Groups: Go Science
Hint: ED has more residues than given

The chain you can see in the electron density is longer than the given chain of amino acids. If you directly start to fit one end of the chain into the density, the residues won't fit properly.
It looks like that there are about 5-6 residues missing after residue 114 (C-terminus) and about 4 residues missing before the first residue (N-terminus).

spmm's picture
User offline. Last seen 41 weeks 18 hours ago. Offline
Joined: 08/05/2010
Groups: Void Crushers

Thanks Batz I think I saved the first one I did...

Joined: 05/19/2009
Groups: Contenders
residu 114 cannot be changed from loop

There is also something odd about residu 114. It cannot be changed. It will remain a loop. Residu 1 does not have this limitation. Is this intentional or an artifact ?

gitwut's picture
User offline. Last seen 41 weeks 4 days ago. Offline
Joined: 05/18/2012
Groups: Contenders
Not a fan

Sorry, but I really dislike ED puzzles, and this one is no exception. There is always too much clutter. If it were possible to toggle sidechains on/off on the cloud it would probably be easier. This cloud is better than most of the previous EDs, but I might do as well or better working it as a denovo.

I know that seeing the sidechains can occasionally give extra clues, but when trying to determine the SS/backbone, they're more a hindrance than help.

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