Violations from ideal values as well as from the average are a measure of structure quality. The menu block "ANALYSIS" provide tools to map violations and deviations on 3D-image of a structure by utilizing color code. From blue, over red to yellow, dark blue being the best and yellow the worst. Seeing the whole spectrum means that distribution of deviations is continuous, whereas only a few colors mean that something should definitively be done with the model.
There are two pairs of modes ("GRP_RESI", "GRP_ATOM" and "BY_FORCE, "BY_ENERG") and two major kinds of analysis, B-value ("ANA_TEMP") and interaction energy ("ANA_ENER)". The results are displayed with the "ANA_IMAG"and centered on the worst (yellow) part"and centered on the worst (yellow) part.
The "ANA_BOND" and "ANA_ANGL" do not display but write to the terminal the statistics about deviations from each particular force field parameter term and the mean deviation for "BONDS" and "ANGLE" energy terms.
Use "ENERGY" menu block to switch on and off particular energy terms.
The menu block "ANALYSIS" is loaded with the file MAIN_CMDS:load_analysis.com.
When RESIDUE mode is on, interaction energy as well as B-value analysis are calculated on a residue basis (averaged over all atoms in a residue.)
When ATOM mode is on, interaction energy as well as B-value analysis is performed and displayed for each atom.
Performs a temperature factor (B-values) analysis.
MAIN_CMDS:anal_temp.cmds is the default macro.
The FORCE mode is the primary mode for energy analysis.
When the FORCE mode is on, energy of the structure is calculated only once and its derivatives are analyzed. The FORCE mode is particularly useful to spot bad contacts using the VdW energy term.
The FORCE mode does not make sense for analysis of electrostatics and density terms, where the direction of derivatives is important and not only its magnitude.
When the ENERGY mode is on, interaction energies for each atom or residue with the surrounding parts are calculated.
The ENERGY mode is the alternative for the FORCE mode. It can, however, be much more time consuming - particularly for calculation of non bonding interactions.
Performs the interaction energy analysis on atom or residue basis along the chain.
and displays color coded analysis on the screen.
MAIN_CMDS:anal_ener.cmds is the default macro.
The color codes of residues of your molecule are relative - from the lowest to highest value: blue means low values and yellow means high values. An equilibrated system should have the whole spectra. Especially bad are the yellow residues when the rest of color spectrum apart from blue is not present at all.
By default "AVERAGE" values are used for color coding. You can change this by using your own macro.
Configurable macro, which creates chosen top violators of analysis mode written into the macro "center_next.com" accessible by clicking "CENT_NEX" or using the keyword shortcut go "g". It is a user friendly way of doing the structure validation using the other analysis flags by the addiiton of sorting, top most violators and sigma cutoff.
This item will eventually replace all analysis menus.
ANA_BOND performs and writes the results of deviations of covalent BOND terms for the current force field parameters. At the bottom the overall deviations are shown. Use this to estimate the scale of the x-ray energy term (ENERGY DENSITY SCALE).
MAIN_CMDS:anal_param_bond.cmds is the default macro.
ANA_ANGL similarly as ANA_BOND performs and writes the results of deviations of ANGLE terms for the current force field parameters. At the bottom the overall deviations are shown. Use this to estimate the scale of the x-ray energy term (ENERGY DENSITY SCALE).
MAIN_CMDS:anal_param_angle.cmds is the default macro.