Posts

Streamlining the RosettaScripts Interface: RosettaScripts Type-hinting in VS Code

~  contributed by  Dr. Vikram Mulligan RosettaScripts Type-hinting in VS Code By Dr. Vikram Mulligan, Research Scientist, Flatiron Institute The RosettaScripts scripting language began as a loose XML-like language with informal syntax, with each Rosetta module defining its own XML interface.  This made it difficult to ensure that Rosetta could handle bad inputs correctly: often, typos or nonsensical inputs were simply ignored, and users were not alerted about problems in their scripts.  This was solved by formalizing the XML interface with an XML Schema Definition (XSD), a project led by Dr. Andrew Leaver-Fay a few years back.  We now require any Rosetta module with an XML interface to provide a machine-readable description of the XML interface, permitting automated checking of syntax, unused inputs, etc., and allowing informative error messages. Rosetta now automatically interrogates all of its own modules on startup and constructs a unified XSD for the entire RosettaScripts language.

Streamlining the RosettaScripts Interface: SimpleMetrics in protocols

~  contributed by Dr. Rocco Moretti SimpleMetrics in protocols By Dr. Rocco Moretti, Associate Professor, Meiler Lab, Vanderbilt SimpleMetrics are a flexible way to perform analysis on your structures. They are a much cleaner way of performing such an analysis when compared to the previous approach of commandeering the reporting functionality of RosettaScripts Filters. However, the initial implementation required that any SimpleMetric be accessed through the RunSimpleMetrics mover. This meant that using SimpleMetrics was sometimes more laborious than using an equivalent Filter, due to Filters being accessible directly from the PROTOCOLS section of the RosettaScripts XML. To make SimpleMetrics easier to use, a `metrics` attribute was added to the `Add` tags in the PROTOCOLS section. This way, adding a SimpleMetric report as a stage in the protocol is as easy as adding an additional Mover or Filter. One consideration in this implementation is how to determine the name under which the r

Streamlining the RosettaScripts Interface: Integrated Logic Selection and LogicSelector

~  contributed by Dr. Jared Adolf-Bryfogle and Frances Chu Integrated Logic Selection  By  Dr. Jared Adolf-Bryfogle, Principal Scientist, Protein Design Lab, Institute for Protein  Innovation RosettaScripts has progressed to become one of the main interfaces to the Rosetta Software Suite.  Within RosettaScripts, there are a number of different sections that enable customized protocols.  Two of the newest components are ResidueSelectors and SimpleMetrics .  ResidueSelectors allow one to select a group of residues based on some criteria, while SimpleMetrics allow one to output a variety of metrics for each molecule under consideration, with many of them being per-residue metrics. I introduced SimpleMetrics to make benchmarking and analysis tasks easier.  For simple tasks, a single ResidueSelector is usually sufficient, but for more real-world applications, one usually would need to define large logic strings to get at the residues of interest.  This would be accomplished by individual s

How to Improve Psychological Safety in Your Lab

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  ~ contributed by JEDI Committee Overview of Psychological Safety Psychological safety was first described over thirty years ago and has been defined as the “shared belief that the team is safe for interpersonal risk taking” (Edmonson, 1999). People of backgrounds historically excluded from STEM are more likely to feel uncomfortable taking risks and sharing their ideas. Thus, p sychological safety is a key component of JEDI efforts. Haris Domond of Equity Impact Associates spoke at winter RosettaCon 2021 on translating psychological safety practices from the corporate environment to the lab workplace. Actionable recommendations from Haris Domond, MTS: Create Individual Development Plans for lab personnel/trainees Publish organizational/lab demographic summary data in transparent manner Clearly define PhD Program requirements and success milestones Distribute projects equitably such that all students have opportunities to do high-impact work Be transparent about your goals when criti

The eternal debate – one score function to rule them all?

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~ contributed by Julia Koehler Leman Molecular modeling packages use various types of score functions, depending on the task and their required atomistic level descriptions. For instance, molecular dynamics simulation packages often use a molecular mechanics force field to model small molecules, peptides and small proteins, and allow exploring the folding trajectory of the latter two. The modeling of chemical reactions requires a description of the electron configurations through quantum-mechanical force fields, which are expensive to compute and only possible for small systems. A combined QM/MM (quantum mechanics / molecular mechanics) approach allows modeling chemical reactions in larger systems such as enzymes. Monte-Carlo simulation packages often rely (at least partly) on knowledge-based score functions that are statistically derived from experimentally validated datasets through an inverse Boltzmann relationship (see Figure).   Figure: Most prevalent scor

Standing up against hate and acts of violence

~ contributed by the Rosetta JEDI committee~ Dear all, Along with all members of our community, we are heartbroken by the recent murders, acts of violence, and discrimination against people of Asian and Asian-American descent. We condemn the increased racism and xenophobia directed at people of Asian and Asian American descent. We stand in solidarity and support with the Asian, Desi, Pacific Islander, and Asian-American members of our community, condemn these acts, and mourn those lost. The recent attacks are the latest forms of bias rooted in hate against people based on their race, religion, ethnicity, socio-economic status, gender identity or expression, and sexual orientation. We call on the entire Rosetta Commons community to stand up against all forms of hate, bias, and bigotry and to eliminate xenophobic rhetoric when it arises. For anyone in the RC community who may feel unease or anxiety as a result of these and other incidents, we hope you will seek support through your unive