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

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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 3 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
User offline. Last seen 23 weeks 3 days ago. Offline
Joined: 08/05/2010
Groups: Void Crushers
Drat

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 2 hours 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
Supported by: DARPA, NSF, NIH, HHMI, Amazon, Microsoft, Adobe, RosettaCommons