Maestro User Manual

Appendix E: Property Names

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any remaining underscores are replaced by spaces. The display name for atom properties is

shown in option menus for selection of an atom property, for example.

Table E.1. Mappings for the author field in the internal name.

Author

Family Name

Author

Family Name

canvas

Canvas

mopac

MOPAC

combgen

CombiGlide

pdb

PDB

des

Desmond

phase

Phase

epik

Epik

ppw

Protein Preparation Wizard

glide

Glide

psp

Prime

glideres

Glide Residue Interactions

pspIFD

Induced Fit

i

Impact

px

PrimeX

ionizer

Ionizer

qp

QikProp

j

Jaguar

qpld

QPLD

lp

LigPrep

qs

QSite

lsbd

LSBD

sd

SD

m

Maestro

sitemap

SiteMap

mcp

MCPRO+

strike

Strike

mmod

MacroModel

user

Added by user

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Maestro User Manual

Glossary

ASD—Atom Selection dialog box.

ASL—Atom Specification Language.

button menu—The menu available from a toolbar menu button, which you open by holding

down the left mouse button. 

clipping planes—The planes that define the displayed depth of the structure. Atoms are

clipped (not displayed) if they are in front of the front clipping plane or behind the back clip-

ping plane. The position of these planes is displayed in the clipping planes window.

current working directory—the directory that is used to write job files (the 

job launch direc-

tory

) and the directory that is used by default in file selectors for reading and writing files. Also

called the working directory.

entry—A structure or set of structures and associated properties. Entries are represented as a

row in the Project Table, and can be used as input for jobs.

ESL—Entry Specification Language.

exporting—Writing structures and their associated data from a Maestro project to a structure

file, or writing data from a Maestro project to a spreadsheet file.

filter—An ESL expression that is used to select, or filter, entries in the Project Table.

grow bond—The bond that is replaced when you add a fragment to a structure in Grow mode.

The grow bond is displayed as a green arrow in the Workspace.

importing—Reading structures and their associated data from a structure file into a Maestro

project, or reading data from a spreadsheet file into a Maestro project.

inclusion—Display of entries in the Workspace. Multiple entries can be included in the Work-

space. The inclusion state (included, excluded, or fixed) is indicated in the 

In

 column of the

Project Table.

isovalue—the value of a property that defines a surface. The property is a function of the three

spatial coordinates, and is represented as a set of points on a three-dimensional grid. 

job directory—The directory that is used to write temporary files for a job. Also known as the

temporary directory or the scratch directory for a job. This directory is created for the job and

removed at the end of the job, unless options are set to preserve it.

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Glossary

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launch directory—The directory that is used to write input files for a job, and to which the

output files from a job are copied when the job finishes.

ligand—(1) A small molecule that is considered capable of binding to a protein. The definition

of a ligand is determined by the ligand detection settings (see 

Section 7.6.3 on page 159

),

which are encoded in the ‘ligand’ ASL expression. (2) A molecule that binds to a metal.

Ligands in this sense are not necessarily covered by the biochemical definition: for example,

CO is considered a metal ligand but does not match the usual ligand detection settings. 

Maestro resources directory—The directory (folder) that contains the default resource files

used by Maestro. This directory is the maestro-vversion/data/res directory of your

Schrödinger software installation.

Maestro user resources directory—the directory (folder) in which resource files for Maestro

are kept that are specific to a user, rather than for general use. This directory is defined as

follows

where vv is the two-digit Maestro version number (92 for this release). $HOME is usually set to

/home/

username on Linux and /Users/username on Mac OS X. %APPDATA% is the location

of shared data on Windows, C:\Users\username\AppData\Roaming.

menu button—A toolbar button that has a menu, which you open by holding down the left

mouse button. The button has a black triangle in the lower right corner. 

option menu—A drop-down menu from which you can select an option. Clicking the button

on the menu displays the menu without having to hold down the left mouse button. 

picking—Selecting atoms in the Workspace.

profile—(1) a named set of customizations of Maestro; (2) the directory (folder) in which

resource files for Maestro are kept that are specific to a Maestro profile, for example, menu and

toolbar customization files. This directory is the profile/profile-name subdirectory of your

Maestro user resources directory.

project—A collection of related data, such as structures with their associated properties. The

project may include data that does not appear in the Project Table.

Project Table—The table that displays the contents of a project, with rows of entries and

columns of properties. The table is located in the 

Project Table

 panel. 

Linux, Mac:

 $HOME/.schrodinger/maestrovv

Windows:

 %APPDATA%\Schrodinger\maestrovv 

Linux, Mac:

 $HOME/.schrodinger/maestrovv/profiles/profile-name

 

Windows:

 %APPDATA%\Schrodinger\maestrovv\profiles\profile-name 

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