Desmond Tutorial

Desmond Tutorial
Learning the Maestro-Desmond Environment
The project directory has a compressed, back‐up copy of the entire project, but it is good
practice to keep around a separate back‐up copy of important project directories,
because sometimes files in the project directory can get corrupted rendering the project
unreadable.
Useful Tools in Maestro
With no aim at providing a complete list, here are some useful tools you might want to
explore. Note, however, that the tools under the Applications menu require separate
licenses from Schrödinger, LLC.
• Maestro > Save Image saves a high quality screen capture of the workspace.
• Project > Make Snapshot saves the current state of a project so it can be recovered
later if necessary.
• Edit > Clean Up Geometry quickly generates a reasonable 3D‐model of a structure
that was drawn by hand.
• Edit > Command Script Editor is a powerful yet simple scripting tool. Each Maestro
command you execute (including graphics tasks) is saved during a Maestro session.
The Command Script Editor allows you to cut‐and‐paste selected commands and save
them in an executable script. For example, if you apply a sophisticated rendering
scheme on a protein complex structure and want to repeat the same rendering on
some other system at a later time, the corresponding sequence of commands can be
saved in a script and applied to the new system. Use of the Command Script Editor
does not require any knowledge of the Maestro command language.
• Display > Surfaces generates a variety of molecular surfaces that can be added to
the Project Table.
• Tools > Sets defines arbitrary sets of atoms to be used for quick rendering or different
kinds of computations.
• Tools > Protein Structure Alignment automatically superposes homologue protein
structures. This is useful when you want to bring multiple X‐ray structures from different
labs into a common coordinate frame using protein structure alignment.
• Tools > Protein Reports generates an extensive table of useful structural information
for the selected entry.
• Applications > Glide is a versatile, fast docking tool.
• Applications > LigPrep prepares small molecules by fixing bond orders, protonation
and tautomerization states, stereo chemistry, and so on.
• Applications > MacroModel provides a plethora of molecular mechanics tools
including large scale conformational searches, flexible docking, free energy calculations,
and so on. MacroModel can be used with a variety of different force fields and
implicit solvent models.
• Scripts menu. Virtually all of Maestroʹs functionalities can be accessed directly from
Python scripts. Maestro provides a straightforward mechanism for implementing
these scripts so that they become permanent, menu‐driven options in Maestro.
There is an extensive library of Maestro scripts that can be downloaded from the
Schrödinger website (www.schrodinger.com) and that is continuously updated and
expanded. To install scripts, select Scripts > Update and select scripts to include, as
26 D. E. Shaw Research September 2008