Joined: 05/09/2008
Groups: None
Additional info about this CASP Roll target

Here is the CASP link for this target (showing the amino acid sequence):


Here is the sequence logo predicted by the SAM server.

H = helix
E = sheet
C = loop (or coil)

The taller the letter at each position, the higher the probability of that specific secondary structure for that amino acid.

For example, the Valines at residues 18, 54, 79 and 100 is highly predicted to be part of a helix. However, the Valine at residue 111 is not predicted to be anything!

The above predictions are already on the starting extended chain which is available in the Alignment Tool (based on the horizontal lines in the above figure).

Joined: 05/06/2011
Groups: None
The information about this puzzle is incorrect, or ...

The puzzle information states: "this round only GUI scripts are allowed." This is not correct I am seeing regular LUA scripts run just fine.

Joined: 05/09/2008
Groups: None
Thank you for catching that bendbob

Sorry about that, the description should be correct now!

Joined: 05/18/2008
Groups: None
the alignment tool doesn't give the structure

and the extend is not is the reset cycle.

Joined: 12/16/2010
new public Recipe: 717 comment structs ...
Joined: 05/09/2008
Groups: None

Because the Rosetta Server models do not match the secondary structure predictions, I did not want to bias you with Rosetta's structure.

The extended chain is only available in the alignment tool (for those who want it) but I did not want some players to randomly start with the extended chain if they didn't know they could reset to get a better model.
This is how we normally post CASP ROLL puzzles starting from Server Models (Puzzle 654, for example).
The extended chain does have the secondary structure predictions on it, however.

Thanks you gramps for providing that script for everyone!

Joined: 05/18/2008
Groups: None
The alignment tool doesn't give the structure

The alignment tool doesn't give the structure

Joined: 05/09/2008
Groups: None
that is indeed a bug!

I'm very sorry about that marie_s, I checked this before posting it, but clearly this isn't working correctly!

I'll look into what is going on, thankfully everyone can use gramps' script for now (good thing this wasn't a GUI-only round!)

Joined: 09/22/2011
Groups: Beta Folders

I haven't been able to access puzzle for days.
Crashes on loading. Whole program crashes to desktop

Joined: 05/09/2008
Groups: None
I am very sorry to hear that, dbuske

Can you post your log.txt after the crash here:

Hopefully we can figure out the issue!

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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