EvalScore reads a score file that contains:
Each line in the score file is of the format:
refstruct/modelstruct(Tab)score1(Tab)score2where refstruct and modelstruct are the filenames of reference and model PDB files in the same directory as the score file. If the actual name of a PDB file includes the “.pdb” suffix, that part can be omitted from the name given in the score file. The score1 and score2 values are floating-point numbers. The “/” and (Tab) characters must be present.
Simply opening a score file automatically starts EvalScore, generates the plot, and connects the plot to the structures. The file type can be indicated by the suffix .score (part of the filename) or the prefix score: (used in the command line, not part of the filename).
The background color of the Chimera window is initially set to a dark gray, but can be changed as desired.
Each predicted structure is represented by a dot on a 2D plot with X = score1 and Y = score2. Initially, all of the dots are red. When the mouse focus is in the plot, the X,Y coordinates of the cursor are reported on the lower right. It may be necessary to click into the plot window to give it the mouse focus. Clicking on a dot makes it blue and shows the reference and corresponding model structures in the main Chimera window, with the reference on the left (at least initially). In the plot window, a “swoosh” mark is drawn from the dot to information above the plot about the structures and scores.
Secondary structure elements (SSEs) in the reference structure are assigned successive colors along the rainbow in N→C order starting with blue and ending with red. Residues in the predicted structure are colored to match those in the reference; a given residue will be the same color in both structures regardless of any helix and strand assignments in the predicted structure. To generate the initial view, the structures are superimposed and then translated apart so that their orientations will be as similar as possible (details...).
By default, both structures will orbit a single center of rotation, but they can be made to rotate around individual centers using the command set independent or the Rotation tool.
Below the plot are standard plot navigation icons provided by matplotlib. Clicking Close dismisses the plot window; Help opens this manual page in a browser window.
To generate the initial view, the predicted structure (model #1) is superimposed onto the reference (model #0) and then translated to the right, as if the following commands were executed:
mm #0 #1 ssFraction false computeSS falseThe focus command ensures that the entire structures are visible in the Chimera window.
move x 50 model #1; focus