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...
by Elizabeth Swanberg | Jan 15, 2019 | FAQs
This is a top priority for Cyrus, and we are currently beta testing a general implementation. We expect a release in Q3...
by Elizabeth Swanberg | Jan 15, 2019 | FAQs
In order for Bench to give useful results, the input structure does need to be accurate. For Good Results: Crystal structures should ideally have resolution at or better than 2 Ångstroms. For Usable Results: Crystal structures with a resolution of approximately3.5...
by Elizabeth Swanberg | Jan 15, 2019 | FAQs
Cyrus products were built to run on Google Chrome. If you are unable to use Chrome, Firefox is your best...
by Elizabeth Swanberg | Jan 8, 2019 | FAQs
The version of Rosetta underlying Cyrus Bench CAD is e3f2cae19743fcd2ee7452da25072bb3b4a639f9, which dates to April 27, 2017. Exception: The version of Rosetta that the DDG metric is currently running is 981ca1ab37cf1092da719de54cee4cfd8a73867e, released on July 23,...
by Elizabeth Swanberg | Jan 8, 2019 | FAQs
We are currently working on displaying the alignment in the structure viewer in Homology, but currently the best option is to read the alignment JSON file in a text editor that supports monospaced font (we use Atom). Once you’ve made sure that the alignments are...
by Elizabeth Swanberg | Jan 8, 2019 | FAQs
Yes, in November 2016 this feature was added to Homology. Click on any number of models on the left, and they will appear superimposed in the...
by Elizabeth Swanberg | Jan 8, 2019 | FAQs
Yes, there is a minimum of 50 residues and a suggested maximum of 1000 residues for Homology Modeling runs. In order to model larger structures, we suggest separating domains, e.g. through BLAST, and running these as individual targets. Run time will range from a...
by Elizabeth Swanberg | Jan 8, 2019 | FAQs
No, if you would like to abort a job email support and we will stop it. We are looking into allowing users to stop Homology Modeling runs before significant computation has been spent on the...
by Elizabeth Swanberg | Jan 8, 2019 | FAQs
During the simulation the metal ions are removed however HM has constraints to the backbone of the templates that helps to preserve the open/close conformations. Once we implement template selection you will be able to select the templates that match the conformation...
