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


101abiogenesis 78 82  7,50412
102ecali 78 1431  7,49512
103BeImmie 78 1431  7,49111
104tallguy-13088 78 1431  7,48411
105arginia 78 1431  7,47411
106girltano 78 1431 Italiani Al Lavoro7,41111
107hoglahoo 78 1431  7,40910
108eromana 78 816  7,40910
109Cerzax 78 1431  7,39710
110Andi1960 78 1431  7,3809
111Continental_Drift 78 1431  7,3709
112Kevonni 78 1431  7,3649
113Merf 78 53  7,3589
114tornado163 78 1431  7,3059
115Protocell 78 1431  7,2638
116Brett Burk... 78 1431  7,2498
117Amphimixus 65 423 7,2358
118NotJim99 63 529  7,2298
119Alistair69 47 193 L'Alliance Francophone7,1917
120Jinxtedium 78 1431  7,1677
121JUMELLE54 78 1431  7,1677
122juram2015 78 1431 StructuralBiology-CHEM4907,1657
123brgreening 78 1431 Beta Folders7,1597
124navn 78 330  7,1596
125mitarcher 78 295  7,1436

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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 1 day 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 32 weeks 3 days 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 32 weeks 6 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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