A params file (with the extension .params) is used to define molecules in Foldit. The params file format is defined by the Rosetta software that provides many functions in Foldit.
Foldit's basic configuration includes many params files. For example, there's a file "ALA.params", which defines the structure of the amino acid alanine.
There are also puzzle-specific params, which include "ir_puzzle" as a part of their name. For example, there's "0000997806.ir_puzzle.params", which contains definitions used in puzzle 997806, otherwise known as 903: Brain Cancer-Related Phosphorylated Id2. The puzzle contained one modified amino acid, a phosphorylated version of serine. The params file defined the configuration for this specialized molecule.
Puzzle-specific params files are most commonly used to define ligands.
A params file contains several types of lines or records. Each line is identified by a keyword such as ATOM, BOND, or ICOOR_INTERNAL.
See an overview of params files in the Rosetta documentation for a detailed discussion of the record types and their meaning.
The sections below give a quick overview of the key ATOM, BOND, and ICOOR_INTERNAL records.
For the phosphorylated serine in puzzle 903, the first few ATOM records were:
ATOM N Nbb NH1 -0.47 -0.350 ATOM CA CAbb CT1 0.07 0.100 ATOM C CObb C 0.51 0.550 ATOM O OCbb O -0.51 -0.550 ATOM CB CH2 CT2 0.05 0.000 ATOM OG OH ON2 -0.66 -0.490 ATOM P Phos P 1.50 1.500 ATOM O1P OOC ON3 -0.78 -0.78 ATOM O2P OOC ON3 -0.78 -0.78 ATOM O3P OOC ON3 -0.78 -0.78
(The hydrogen atoms are not included in this example.)
The first field after the ATOM identifier in each line is the name assigned to the atom. Usually, the name is based on the atomic symbol, so the name for backbone nitrogen happens to be "N". Names must be unique, so the the alpha carbon is called "CA", and the beta carbon is called "CB", while the carboxyl carbon is just "C". The names are used in the BOND and ICOOR_INTERNAL records, as described below.
The next field in the ATOM record is the Rosetta atom type, which is "Nbb" or "backbone nitrogen" for the same atom. See Determining Rosetta Atom Types, which includes examples showing the atom types for all of the standard amino acids.
Some of the more common Rosetta atom types include:
|Cabb||alpha carbon (backbone)|
|CObb||carboxyl carbon (backbone)|
|OCbb||carboxyl oxygen (backbone)|
|Haro||hydrogen attached to aromatic carbon|
|Hapo||apolar (non-polar) hydrogen|
After the Rosetta atom type, there's the CHARMM atom type, for example "NH1" or "CT1". It's unknown whether these names are used in Foldit.
The remaining two fields in the ATOM record are described as partial charges. Again, their significance in Foldit is not known.
The BOND records define which atom is connected to which. The names assigned in the ATOM record are used.
For the phosphorylated serine, the first few BOND records were:
BOND N CA BOND N H BOND CA C BOND CA CB BOND CA HA
The first BOND connects the backbone nitrogen to the alpha carbon. The second BOND connects the backbone nitrogen to a hydrogen, which was not shown in the ATOM records example. The next three BOND records connect alpha carbon to the carboxyl carbon (C), the beta carbon (CB), and a hydrogen (HA), which was also not included in ATOM record example.
The ICOOR_INTERNAL records give the "internal coordinates" of each ATOM defined in an ATOM record.
The first field after the ICOOR_INTERNAL keyword is the atom name, which is followed by two angles (Phi and Theta), and a distance (in angstroms). There are then three more atom names, the "parent atom", "angle atom" and "torsion atom".
The following brief excerpt shows the ICOOR_INTERNAL records for the backbone nitrogen and the alpha carbon:
ICOOR_INTERNAL N 0.000000 0.000000 0.000000 N CA C ICOOR_INTERNAL CA 0.000000 180.000000 1.458002 N CA C
The example shows how the backbone nitrogen is the base of the other coordinates, so the angles and the distance are zero.
The Rosetta article "What are "internal coordinates" and why does Rosetta use them?" describes the numeric values in more detail.
The specific numeric values in the ICOOR_INTERNAL records are generally not available in Foldit, but they of course affect where the corresponding atoms appear in the user interface. Also, the approximate Phi angle can be seen in the Rama Map in Foldit.