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RosettaCommons / tools

Tools for parsing Rosetta source code and scripts for running specific Rosetta applications.
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Add the nanobody 4w6w to the outlier_list #73

Closed d8vela closed 5 years ago

d8vela commented 5 years ago

Add the nanobody 4w6w to the outlier_list so that it will be black listed from being used as a template in antibody.cc. We found that this template (nano body) was problematic because and causes antibody.cc run to fail because it was trying to graft a H2 loop from this template that had a cysteine that is part of a disulfide with other parts of the non-grafted segment of the nanobody framework. We find that in previous versions of the the PDB (before 2012), this template (4w6w) would not be selected and so antibody.cc would run successfully.

roccomoretti commented 5 years ago

Was this intended to go to the main RosettaCommons repo? -- Doesn't sound like a bad change, I just wanted to check intent. (Xref: @smlewis).

indigogo commented 5 years ago

Yes, we are finding that the antibody grafting code cannot even load this template, and if it blast gets a hit on it, it leads to a system exit which terminates the program.

On Wed, Sep 26, 2018, 17:30 Rocco Moretti notifications@github.com wrote:

Was this intended to go to the main RosettaCommons repo? -- Doesn't sound like a bad change, I just wanted to check intent. (Xref: @smlewis https://github.com/smlewis).

— You are receiving this because your review was requested. Reply to this email directly, view it on GitHub https://github.com/RosettaCommons/tools/pull/73#issuecomment-424914807, or mute the thread https://github.com/notifications/unsubscribe-auth/AEPD6En9PYrhmK497uaUskvrBZgxKAo3ks5ufBwsgaJpZM4W7s8O .

d8vela commented 5 years ago

Yes. We find that the only problem with this scaffold 4W6W is the H2 portion of it and not the others (as far as we know). So, what we want to do is just block the H2 loop from being considered in the list of candidates that are possible for being selected in the loop grafting step.

The additions for comments in the outlier_list sounds useful! But, I don't actually prefer not to be the one responsible to making these changes.