Ask the Scripts Expert: Color by Entry, Creating Custom Scripts, and Training ResourcesDr. Christopher Higgs, Senior Applications Scientist
Dr. Christopher Higgs is a Senior Applications Scientist and works closely with researchers using Schrödinger software for molecular modeling and drug design projects. Dr. Higgs has an extensive amount of scripting experience and is our in-house Scripts Expert.
Q. I'd like to color the atoms in my entry based on their charge or other properties. Is it possible to do this in Maestro?
A. Included in our 2015-3 software release, we have developed a new GUI that will allow you to color atoms, residues, chains, etc. by a selected property in the Project Table. This property can be divided into a number of bins (up to 5 bins), while the user can control the binning width and color.
To access this script from within Maestro, select Scripts → Project Table → Color by Entry Property...
Q. I am interested in writing my own Python scripts, are there any resources available to help me get started?
A. Under the Maestro → Help menu, there are two helpful links. The first, “Python Module Overview” gives a nice introduction to some of the basics of using Schrödinger's API. This includes working with structures (I/O, manipulation, and analysis etc.), developing scripts to run from Maestro and also working with specific applications (i.e. MacroModel, Jaguar and Canvas). The second link, “Python API Reference” gives you the full documentation on our API. In addition, we are planning on holding training workshops and seminars on our API in the near future. Please check our website for announcements.
Q. I'd like to modify one of the pre-installed scripts. Is it possible to do this and where can I find the source files in my installation?
A. Yes, it is possible to do this, although it is recommended to make a local copy of the script first. All of the distributed Script Center scripts can be found in $SCHRODINGER/mmshare-v*/python/common/. These scripts can also serve as starting points for developing you own custom scripts.
Q. I'm interested in creating a custom script, but I don't have the time or resources. Can I request new scripts from Schrödinger?
A. Absolutely! Simply contact us at firstname.lastname@example.org or speak with you local Application Scientist. In many cases, script requests can be turned around in 24-48hrs, depending on the complexities of the request.