Maestro User Manual

Chapter 3: Importing and Exporting Structures and Data

Schrödinger Software Release 2015-2 

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SMILES

Import SMILES strings from a text file with a .smi extension or a compressed text file with a

.smigz

 or a .smi.gz extension. The text file must have one SMILES string per line, with an

optional title separated by a blank. The structures created on import are 2D structures with

hydrogens, so you must convert them to 3D structures before using them in applications. 

Jaguar Input 

Import from Jaguar input files, which have .in extensions. 

ReagentPrep

Import ReagentPrep structure files, which have .bld extensions. These are special files labeled

with grow bonds for use in CombiGlide.

MacroModel

Import from MacroModel input or output structure files, which have .dat or .out extensions.

Properties are imported as well as structures.

Jaguar Output

Import from Jaguar output structure files, which have .out extensions. Properties are imported

as well as structures.

MCPRO Input 

Import from MCPRO

+

 input files, which have .zmat extensions. 

Desmond 

Import Desmond composite model system files, which have a .cms extension if uncompressed,

or a.cms.gz, or .cmsgz extension if compressed.

Glide Pose Viewer

Import Glide pose viewer files, which are Maestro files that have the receptor as the first entry,

followed by a set of docked ligands. These files have a _pv.mae extension if uncompressed,

and _pv.mae.gz or _pv.maegz if compressed. There 

Other formats: 

Import structures from a range of other programs or formats, including BioGraf, GAMESS

output, Gaussian, Mopac, XYZ (MYZ is a synonym for multiple structures in XYZ format),

CCF, CIF, mmCIF, and FHI-aims. The format conversion is performed with the use of the

program Babel. The list of formats provided here is a subset of the formats that Babel can

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Chapter 3: Importing and Exporting Structures and Data

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convert. If you want to import structures in formats not listed here using Babel, you can use

Jaguar to read the files. See 

Section 11.1.2

 of the Jaguar User Manual for more information,

including the full list of file types read by Babel. 

On Linux hosts you can use Babel from the command line to convert structures to a format that

Maestro can import directly. To do so, you must first set the environment variable BABEL_DIR:

To obtain usage information, enter the babel command without arguments:

$SCHRODINGER/mmshare-v

version/bin/platform/babel

Here, version is the 5-digit mmshare version number, and platform indicates the platform on

which you are running, e.g. linux-x86.

Any

Import a file of any type. The file type is determined from the extension of the selected file or

the file name you enter in the 

Selection

 text box. If the extension is not unique, Maestro does

not import the file. The formats for which Maestro recognizes the extension are Maestro, Mol

and Mol2, PDB, SD, XYZ (or MYZ), Mopac Cartesian and Internal, and Spartan. This option

is useful if you want to locate any of these kinds of structure files. 

Filtering the file list: To filter the list of files according to your own requirements, choose

Custom File Filter

 from the 

Files of type

 option menu. The 

Custom File Filter

 dialog box opens,

in which you can enter the filter. The filter can include metacharacters for filename expansion:

*

 for zero or more characters; ? for a single character, and square brackets for specific charac-

ters or a range of characters, e.g. [a-e]. 

Selecting a directory: To specify the directory from which to import, you can enter it in the

File name 

text box, or navigate to it using the standard locations, the navigation buttons, or the

option menu at the top of the panel. The path displayed in the option menu and the lists are

then updated for the chosen directory. 

Selecting a file: To select a file, you can type its name (and path) in the 

File name 

text box, or

select it from the list. 

If you type the name of the file in the 

File name 

text box, you must include the correct exten-

sion. In the list of files, only files with the correct extension are displayed.

If the file does not appear in the list, check that you have chosen the correct file type from the

Files of type 

option menu, or select 

All

 from this option menu to view all files. 

csh/tcsh:

setenv BABEL_DIR $SCHRODINGER/mmshare-v

version/data/babel

bash/ksh:

export BABEL_DIR=$SCHRODINGER/mmshare-v

version/data/babel

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Chapter 3: Importing and Exporting Structures and Data

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Selecting multiple files: You can import structures from more than one file at a time. To select

multiple input files, use the 

SHIFT

 and 

CTRL

 keys in combination with mouse clicks to select

as many files as you wish in the 

Files

 list, or click 

All Files

 to select all files in the 

Files

 list.

3.1.2

Selecting Import Settings

Once you have selected the files to import structures from, you must choose which structures

to import and how to display them. The options for these tasks are hidden by default, and can

be displayed by clicking 

Options

. In addition to the options shown in the panel, there are some

options that can be set as preferences in the 

Preferences

 panel—see 

Section 14.2.4 on

page 343

. These options are also described below. 

Selecting structures to import: Maestro can import multiple structures from multiple files. If

you do not want to import all structures from each file, deselect 

Import all structures

. You can

then enter the index of the first structure in the 

Start

 text box, and the total number of structures

to import in the 

Total

 text box. You can import to the end of the file by selecting 

End

 instead of

specifying the total number. These settings are applied to all files: they cannot be set for each

file in a multiple file selection. To import different numbers of structures from a set of files,

select each file in turn and set the number of structures to import. 

If you want to import only the first structure from a Desmond CMS file, select 

For Desmond

files, import only first structure

.

Importing associated data: If the structure file has other data associated with it, the data can

be imported into the project and associated with the relevant entries, by selecting 

Import asso-

ciated data files

. The mapping of the data to the entries is done in a file with the suffix .smap.

This option is selected by default.

Reading alternate positions from PDB files: If the PDB file contains alternate positions, you

can read them by selecting 

For PDB files, read alternate locations

. If this option is not selected,

the coordinates for the atoms with the highest occupancy are read, and the rest are ignored. You

can display alternate positions from the 

Workspace

 menu. 

Creating titles for SD structures: SD files often do not have a title property, so you must

choose one to display in the project from the options under 

For SD files, create titles from

. The

default is SD molecule name. To specify an alternative property for the title, select 

SD property

and enter the property name in the text box. 

Creating groups: Structures can be added to the Project Table as single entries or as groups.

You can control how the entries are grouped on import by selecting an item from the 

Create

groups for

 option menu. By default, groups are created for files with multiple structures. The

groups are named after the file, minus the extension. You can also create a single group for all

structures from all imported files, and provide a name in the 

Group name

 text box.

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