Appendix 2-Specifiers

There are two main forms of specifiers in NAMOT2. You will only encounter the Atom specification if you are working on the command line. The geometry controls accept H:U or H:U:B specifications. On the command line, the HUBA format is the default, to use MCGA format, you must put a single "m" in front of the specifier.

H:U:B:A (Helix:Unit:Base:Atom)
Where each field, except for the Atom field, contains the number of the type to be specified. Possible wild cards are "-",",", and "*".
Examples:
*:1-3:*:*
Specifies all atoms of units 1 through 3 on every helix.
*:1,12:*:*
Specifies all atoms of units 1 and 12 on every helix.
M:C:G:A (Molecule:Chain:Group:Atom)
Where each field, except for the Atom field, contains the number of the type to be specified. Possible wild cards are "-",",", and "*".
Examples:
m*:1:*:P
Specifies the phosphate atoms on all groups of chain 1 on every molecule.
m*:*:1,12:*
Specifies all atoms of groups 1 and 12 on all chains on all molecules.

Specifying atoms

The program understands regex expressions in the atom field. Examples:

"*:1-6:*:C*"-Specifies all Carbon atoms in units 1-6.
"m1:1:*:.*\*"-Specifies all atoms that end with "*" in chain one of molecule one.
"m1:1:*:!.*[EBP\*]"-Specifies all atoms that do not with E,B,P, or "*" in chain one of molecule one. This leaves just the bases themselves.