Name Mappings

The Name mappings text box allows the user to change the name of an atom, residue, ligand, or chain. This may be needed to achieve compatibility with the Amber forcefield definitions used by energy calculations or other reasons. Multiple name mappings can be included, separated by semi-colons. Note, since a common use case is importing files from Schrodinger's Maestro package, these files are automatically recognized and appropriate name mappings employed, saving you the trouble.

For residues and ligands, there are two types of mappings called PDB and AMBER. PDB refers to a 3-letter residue/ligand ID used for display or when exporting files. AMBER refers to the name of an Amber forcefield definition. The PDB name implies the AMBER name, but there are occassions where these want to be different. An example is cysteine where the (default) PDB name is CYS and the Amber name is one of CYS (HS), CYM (S-anion), and CYX (disulfide bridge).
The syntax for the mappings are:
where is 3-letter id>.: as in CYS.301A:A.
For example if CYS 301 on chain B has a disulfide link to another cysteine, the mapping AMBER:CYS.301:B=CYX is used.

Another common use of mappings is to specify histidine types, mapping HIS to Amber types HID, HIE, HIP. If the right side of the equals sign (=) is blank, this means the residue should be removed.
Another use of residue mappings is when you happen to have a file where two different kinds of molecules are given the same name, say MOL, and they need to be distinguished for forcefield assignment.
For example, if MOL.201 and MOL.301 are different kinds of molecules, you might do:

Protein residues or compounds named UNK cannot be used in energy calculations or simulations because, when files are loaded from the PDB, most such molecules are incomplete. If you are sure the molecule is complete, rename it (say, UNK residue number 201) to MYC (or whatever 3-letter code you want) using:

Atom naming mappings are primarily used for hydrogens. Typically, PDB and Amber hydrogen naming is compatible and also consistent with hydrogens added by the commonly-used Reduce program. Other software tools may use different naming conventions. The format of atom name specifications is:
|=,=, ...;
where * means apply to any residue.
For example, *|HXT= would remove any HXT C-terminal atoms.
Other examples,
ASN|HD2=HD22; (different naming convention)
SER|H1=H,H2=; (Change an NH2 terminal to NH)
Note, mappings that just apply to N-terminals or C-Terminals would be specified with a residue spec such as ASN_NT or ASN_CT.

Some other specifications for loading structure files can be provided:
RESET; Clear out any of the default mappings (used if they get in your way).
NOPDB; Don't lookup ligands in the PDB het dictionary for bond definitions (default is to do lookup).
CHAIN:A=Z; Change the chain ID A to Z. A model number may be added to the chain ID as in A1.
MODEL:3; Keep only model 3 in an NMR file (-1 means ignore model records, useful when only one model specified).
ALTLOC:*; Keep the alternate location with the best B value.
Also: ALTLOC:=, where is A, B, C, etc.
INFER: false; Infer bonds (false means don't, default is true)