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


201guygeva2311 84 1577  4,3121
202Primalsoul 84 1577 Gargleblasters4,3021
203tck1988ca 84 1577  4,2991
204Talias 84 1577  4,2971
205NGanes 84 1577  4,2921
206bgiesy 84 1577  4,2871
207AryehK 84 1577  4,2641
208Paltiel 84 1577  4,2601
209perrya 84 343  4,2581
210CaliberDied 84 1577  4,2441
211Ronin-Sensei 84 1577  4,2091
212mannre 84 1577 CHE 476 Advanced Biochemistry Laboratory University of Mount Union4,1371
213zaq1202 84 1577  4,0321
214roman madala 84 549  4,0291
215akii 84 1577  4,0231
216ktyk 84 1577  3,9931
217davidjakubec 84 1577  3,8731
218Otpk 84 1577  3,8351
219basakd 84 1577  3,7681
220EffJay 84 1577  3,6841
221guineapig 84 34  3,5731
222MadTrumpeter 84 1577  3,5541
223KarenCH 84 1577 Anthropic Dreams3,3861
224sushi810 84 1577  3,2061
225bataebi 84 1577  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 week 4 days 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
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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 24 weeks 1 day 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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