Maestro User Manual

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Figure 5.12. The Atom Type (MacroModel) tools in the Atom Properties tab.

5.11.2

Partial Charge

To apply new partial charges to atoms of interest, enter new charges in the 

Partial Charge

 and

Solvation Charge

 text boxes, and use the picking tools to apply the partial charges to the atoms

of interest. Both of these charges are used in MacroModel calculations. The solvation charge is

used in MacroModel GB/SA solvation calculations. Generally, these two values should be the

same. Default values for these charges are supplied with MacroModel force fields. You can

also use partial charges from Jaguar electrostatic potential calculations, which are read by

default when the results Jaguar calculations are incorporated or imported.

5.11.3

PDB Atom Name

A

 

PDB atom name is a combination of a chemical symbol and a connection indicator. The first

two characters contain the element symbol, right-justified; the third character is a remoteness

indicator (A=alpha, B=beta, G=gamma, and so on), and the fourth, if it is needed, is a numeric

branch designator. For instance, the name “_CA_” represents an alpha carbon, “_CB_” a beta

carbon, and “_HB_” a hydrogen on a beta carbon. In these descriptions, the underscore charac-

ters represent spaces, which are required for compliance with PDB semantics: “CA__” is a

calcium atom, and is different from “_CA_”.

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Figure 5.13. The PDB Atom Name tools in the Atom Properties tab.

Occasionally Maestro is not able to assign PDB names to all the atoms. To manually apply

missing PDB atom names, enter the desired name in the 

PDB atom name 

text box and use the

Apply PDB atom name

 picking tools to select the atoms to which you want to apply the name. 

For some purposes, such as for ligands in Prime induced fit calculations, it is useful to have

unique atom names within residues. To make the atom names unique, use the S

et unique PDB

atom names within residues

 picking tools. The unique names are composed of the element

symbol, right justified in the first two characters, followed by a numeric index for that element.

5.11.4

Atom Name

You can assign one of three types of names to atoms in the Workspace: user-specified, canon-

ical, or unique. User-specified names can be any length. To assign a user-specified name, type

the name in the 

Atom name

 text box of the 

Set atom name

 section, and use the picking tools to

apply the name. You must display the atom name labels before you can see the new name.

A canonical atom name is an automatically assigned combination of atom property pairs:

Element & Atom Number

 or 

Residue Number & PDB Atom Name

. To assign canonical names,

select the desired pair of properties from the 

Composition

 option menu, specify a separator

symbol in the 

Separator

 text box, and click 

Apply To All Atoms

. You cannot selectively apply

canonical names.

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Figure 5.14. The Atom Name tools in the Atom Properties tab.

Unique names are generated using the element and atom number of each atom. If this naming

scheme produces atoms with identical names, Maestro adds numeric suffixes, followed by a

tilde (~) to distinguish the names. To apply unique names to all atoms, click 

Make Unique

 in

the 

Modify existing names

 section. As for canonical names, you cannot selectively apply

unique names. 

5.11.5

Grow Name

This name is the name used internally for a fragment when growing a structure. The intended

use of this property is labeling new fragments for a fragment library.

5.11.6

Isotope Number

To set the isotope number (atomic mass number) for selected atoms, choose 

Isotope number

from the 

Property

 option menu. You can specify the isotope in the text box, then apply it to

atoms with the picking tools. The isotope number is used in calculations of molecular weight. 

The isotope can be displayed in an atom label (see 

Section 8.2 on page 162

) in two ways. If

you choose the 

Isotope number

 property to include in the atom label, it is displayed as atom-

isotope, e.g. C-13. If you choose the mass number property, only the atomic mass number is

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displayed. For hydrogen, you can set a preference to display the element label as H, D, or T,

depending on the isotope number—see 

Section 14.6 on page 360

.

5.11.7

Other Properties

When you choose 

Other

, the tools that are displayed allow you to change the properties for any

of the properties that do not have special editing tools. These tools consist of a 

Properties

 list,

which lists all the properties that have values for any of the atoms in the Workspace; an 

Atoms

table, which lists the atoms that you choose for making changes in the properties; 

Add

 and

Delete

 buttons, for adding and deleting properties, and 

Add atoms to edit their properties

picking tools, for adding atoms to the 

Atoms

 table.

Figure 5.15. The Other tools in the Atom Properties tab.

To edit one or more properties:

1. Select the desired properties in the 

Properties

 list. 

The properties are added as columns to the 

Atoms

 table. 

2. Use the 

Add atoms to edit their properties

 picking tools to select the atoms to edit. 

The atoms are listed in the 

Atoms

 table by atom number, and the property columns are

populated with the values. 

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