Maestro User Manual

Chapter 3: Importing and Exporting Structures and Data

Maestro 10.2 User Manual

49

the command line under Unix to extract a structure or a chain into a PDB file. 

Figure 3.2. The Get PDB File dialog box.

To import a PDB file:

1. Choose 

Project

 

→ 

Get

 

PDB

 or click the 

Get PDB

 toolbar button. 

2. Enter the PDB ID in the 

PDB ID

 text box.

The ID can be in lower case or upper case.

3. If you want to download only a single chain, enter the name in the 

Chain name

 text box.

4. Select 

Auto

, 

Retrieve from local installation 

or 

Download from Web

.

Auto

 tries the local installation first, then downloads from the web as a fallback.

5. Click 

Download

.

The structure is copied to your current directory as a PDB file and imported into Maestro, then

the dialog box closes. If you choose to retrieve the file from a local installation, the installation

used is the first found in the following list of locations:

• $SCHRODINGER_PDB 

• $SCHRODINGER_THIRDPARTY/database/pdb 

• $SCHRODINGER/thirdparty/database/pdb 

3.1.7

Error Reporting for PDB Files

When Maestro imports structures from PDB files, it attempts to place bonds according to a set

of standard residue templates, the CONECT records of the PDB file, and geometry. A few

amino acids require that choices be made as to where to place the double bonds and formal

charges. Schrödinger’s conventions for these choices are given in 

Table 3.1

.

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Chapter 3: Importing and Exporting Structures and Data

Schrödinger Software Release 2015-2 

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If the placement of bonds or identification of atoms fails, the regions of the structure in which

problems were identified are assigned an atom property (i_m_pdb_convert_problem) that

records the type of error. This property can be used to color the structure by the conversion

status, with the 

PDB Conversion Status

 color scheme. The color scheme is given in 

Table 3.2

.

This scheme is not used by default, but you can set a preference to color the structure by

conversion status on import in the 

Preferences

 panel—see 

Section 14.2.4 on page 343

.  

Table 3.1. Placement of double bonds and formal charges for imported amino acids.

Amino Acid Pair

Double Bond

 Formal Charge

ARN/ARG

between CZ and NH1

for ARG, +1 formal charge on NH1

ASP/ASH

between CG and OD1

for ASP, -1 formal charge on OD2

GLU/GLH

between CD and OE1

for GLU, -1 formal charge on OE2

Table 3.2. Coloring scheme for structures imported from PDB files.

Color

Description

orange

Non-standard residues connected by geometry and/or CONECT records. Unless 

duplicate CONECT records are specified, only single bonds are assigned, so you will 

need to add multiple bonds.

red

Standard residue, but the input PDB file had missing atoms. 

blue

A standard residue that has some atom names unknown to the standard connection 

template. The unrecognized atom names were connected by geometry. 

cyan

An adjacent residue is listed in the SEQRES records but is entirely missing from the 

ATOM records, indicating a gap in the structure.

green

A residue with alternate positions for the atoms, indicating partial occupancies. By 

default, all sets of positions are read and stored in the entry. The first set is the set that 

is displayed by default. 

gray

Standard residues connected by standard templates. Confidence in bond orders 

assigned to these residues is high. 

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Chapter 3: Importing and Exporting Structures and Data

Maestro 10.2 User Manual

51

Maestro imports PDB files by running the utility pdbconvert, which is described in

Section 1.3

 of the General Utilities manual. The conversion creates a temporary Maestro file,

and imports the structures from this file. Maestro displays warnings to indicate the status of the

PDB conversion, which are listed in 

Table 3.3

. The atom property is stored in the project, and

can be used to select residues in the 

Atom Selection

 dialog box. 

3.1.8

Entry Names for Imported Structures

The names of project entries are not required to be unique. Maestro creates entry names that

are unique within the file imported by appending the index of the structure in the file to the file

base name. Thus, if you import structure 5 from file mystruct.mae, the entry name would be

mystruct.5

. If valid entry names already exist, Maestro does not overwrite them. 

3.1.9

Reading Jaguar Input Files

Jaguar maintains its own input files, which include calculation options in addition to the

molecular geometry, and may also include molecular orbitals. Therefore, Jaguar has a separate

file reading mechanism. When you read input files through Jaguar, the structures are displayed

in the Workspace and Maestro-formatted files are created. 

To read input files through Jaguar, choose a task from the 

Jaguar

 submenu of the 

Applications

menu, then click 

Read

 in the 

Jaguar

 panel. The 

Jaguar Read 

file selector is displayed. Navi-

gate to the directory containing the file, and select the file. Choose the file type from the 

File

Format

 option menu, and change the 

Read as

 setting if necessary. Click 

OK

 to read the file.

For more information, see the 

Jaguar User Manual

. 

Table 3.3. PDB conversion warning messages.

Status 

Message and Explanation

OK No 

message. 

Conversion appears successful.

WARNING

“Problems found while converting file.” A temporary PDB output file was gener-

ated successfully, but the assignments were not all successful. 

ERROR

“Could not convert file to formatname format.” The conversion failed, usually 

because the temporary output file could not be created. There may be a permis-

sions problem, or the disk may be full. Another reason for failure is the attempt to 

convert a file that has varying number of atoms in different MODELs.

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