by Elizabeth Swanberg | Jan 15, 2019 | FAQs
If you are experiencing unusual behavior is CAD, we will be happy to help you fix the issue. Some issues can be resolved by closing all tabs, exiting CAD, and then reopening CAD. Some issues will disappear during this process because they are browser-related (we...
by Elizabeth Swanberg | Jan 15, 2019 | FAQs
When a structure is imported through the Structure Loader, Bench concatenates all chains in the PDB file into a single long string of residues. The chains will be in the same order as they appear in the PDB file. This reflects the protocol used by Rosetta. As a result...
by Elizabeth Swanberg | Jan 15, 2019 | FAQs
The RMSD values provided by Bench are calculated using the alpha carbon positions of the structures being...
by Elizabeth Swanberg | Jan 15, 2019 | FAQs
The scoring metrics from HM and CAD are listed below as they appear left to right (lower is better): Score is a summary of the Rosetta energy function, reported in Rosetta Energy Units. When no other specific considerations apply, this is how one should rank models....
by Elizabeth Swanberg | Jan 15, 2019 | FAQs
The Structure Viewer used in CAD and HM does not have a way to visualize disulfide bonds, but they will still be accounted for by Rosetta during any calculations. We are planning on switching viewers in the future to one that will allow for disulfide bond...
