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


101abiogenesis 79 124  7,50412
102ecali 79 1607  7,49512
103BeImmie 79 911  7,49111
104tallguy-13088 79 1607  7,48411
105arginia 79 1607  7,47411
106girltano 79 1607 Italiani Al Lavoro7,41111
107hoglahoo 79 1607  7,40910
108eromana 79 911  7,40910
109Cerzax 79 1607  7,39710
110Andi1960 79 1607  7,3809
111Continental_Drift 79 1607  7,3709
112Kevonni 79 1045  7,3649
113Merf 79 43  7,3589
114tornado163 79 1607  7,3059
115Protocell 79 1607  7,2638
116Brett Burk... 79 1607  7,2498
117Amphimixus 78 592 7,2358
118NotJim99 59 415  7,2298
119Alistair69 37 168 L'Alliance Francophone7,1917
120Jinxtedium 79 1607  7,1677
121JUMELLE54 79 1607  7,1677
122juram2015 79 1607 StructuralBiology-CHEM4907,1657
123brgreening 79 1607 Beta Folders7,1597
124navn 79 354  7,1596
125mitarcher 79 517  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 6 hours 2 min 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 41 weeks 3 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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Developed by: UW Center for Game Science, UW Institute for Protein Design, Northeastern University, Vanderbilt University Meiler Lab, UC Davis
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