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To open the 

PyMol for Maestro

 panel, choose 

Tools 

→

 View in PyMOL 

in the main window. 

Figure 17.1. The PyMOL for Maestro panel.

Maestro uses the following sources to find an installation of PyMOL to use, in the order given:

1. On Windows, the registry.

2. The  PYMOL4MAESTRO environment variable. This environment variable should point to

the top directory of the PyMOL installation. This is the preferred method of specifying

the location of PyMOL.

3. A PyMOL launch script called pymol4maestro in the Schrödinger software installation.

This script must run PyMOL.

4. A PyMOL installation in $SCHRODINGER/pymol.

5. The standard PyMOL environment variable PYMOL_PATH.

6. On Windows, C:\Program files\pymol\pymol.

7. A launch script called $SCHRODINGER/pymol.

You can choose to send the Workspace structure or the selected entries to PyMOL. These struc-

tures are written to disk and then read by PyMOL, which is automatically started. You can also

start PyMOL without sending structures to it by clicking 

Launch

, and you can then hide or

show the PyMOL panel by clicking the relevant button. 

Once you have structures in PyMOL, you can use the 

PyMOL for Maestro

 panel to perform

some of the PyMOL operations, like appending a scene to the list, stepping through scenes,

updating and deleting scenes. You can choose whether to use ray tracing or rendering for the

image, and save the current image, with the 

Image

 buttons. For the representation, you can use

the closest match to Maestro’s representation with the 

Closest Match

 option, or use PyMOL’s

representation by deselecting this option. You can also use the PyMOL or the Maestro mouse

functions, with the 

Remap Mouse

 option, and show or hide the scene buttons in PyMOL with

the 

Scene Buttons

 option. Finally, you can clear PyMOL, save a PyMOL session, and quit

PyMOL with the 

PyMOL

 buttons.

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If you are running Maestro and PyMOL on a Mac, you can use the X11 version of PyMOL

rather than the native version, by selecting 

Use X11

 in the 

PyMOL for Maestro

 panel.

17.4 ChemDraw and ISIS/Draw

When you copy a structure in ChemDraw or ISIS/Draw, it is placed on the clipboard as an

object with an application-specific MIME type. Maestro recognizes objects with these MIME

types, so you can paste them into the Workspace. The details of how the structure is pasted are

given in 

Section 3.7 on page 61

. You must make sure that all atoms in the structure have

explicit atom types, not generic metals (M) or organic groups (R). 

In ISIS/Draw, you must set an option to enable copying to the clipboard in the appropriate

MIME format. To do so, go to 

Options 

→

 Settings 

→

 General

 and select 

Copy Mol/Rxnfile to

the Clipboard

. 

If you want to paste a structure from Maestro into ChemDraw, you can paste it as a SMILES

string. When you copy a structure in Maestro, it is added to the clipboard as a SMILES string,

which you can then paste into any other application that accepts a SMILES string.

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Chapter 18

Maestro 10.2 User Manual

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Maestro User Manual

Chapter 18:

Help

This chapter describes the various ways in which you can obtain information on Schrödinger’s

products. Maestro has an online help facility, automatic context-sensitive help (Auto-Help),

and tool tips (balloon help). Manuals in PDF format are included with the product distribution,

and each product has a Known Issues page on the Schrödinger web site.

18.1 The Help Menu

The 

Help

 menu in the main window provides access to various kinds of information about

Maestro and Schrödinger products. The items on this menu are described briefly below. Some

of these items are described in more detail in later sections. 

•

Help

—Opens the 

Help

 panel at the default help topic.

•

Documentation Index

—Opens the documentation index file in the Help panel. Click a

link to view a manual or other document in your PDF viewer.

•

Search Manuals

—Opens the full text search index for the PDF documentation in Adobe

Reader. You can then search across all the PDF documentation for words or phrases.

•

Python Module Overview

—Opens the top-level document that provides an overview of

the Python modules supplied for use with Schrödinger software. 

•

Python API Reference

—Opens the top-level document that provides access to detailed

descriptions of the Python modules supplied for use with Schrödinger software.

•

Keyboard Shortcuts

—Displays a help topic that describes use of the keyboard keys in

Maestro.

•

Tips

—Displays a help topic that provides tips for using Maestro.

•

Tutorials

—Opens the 

Tutorials

 panel, in which you can choose a tutorial, copy the files,

and open the relevant manual.

•

New Features

—Displays a file that contains information on the new features in the cur-

rent release. 

•

Known Issues

—Submenu with a list of products for which known issues pages are avail-

able on the Schrödinger web site. When you choose a product from the submenu, the

Known Issues page opens in your browser. If you are not logged on to the Schrödinger

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