Last modified: 5-apr-2004

- Syntax
- INITIALIZE
- APPEND
- ATOMIC
- RESIDUAL
- COORDINATES
- CHARGES
- RADII
- TEMPERATURE
- SET
- SELECT
- INTERNAL
- ENERGY
- POINTS
- PAIR
- PARAMETER
- MAP
- Examples

Analyzed form of data is stored for calculation of average, standard deviation (sigma) and maximal and minimal value for each SELECTED ATOM or RESIDUE record for the specified property. Each record contains five kinds of data: the number of matches, the sum of values, the sum of squared values and the minimal and maximal value. Average value can be later calculated by dividing sum of values with number of matches and standard deviation from square root of record variance divided by number of matches minus one. Record variance is calculated from the sum of square values minus square of sum divided by number of matches. This way possible to process fragments of data sets one by one and yet get statistical analysis of the whole one. These make possible to investigate large data basis that can not be loaded in the program in a single piece.

Average and standard deviation for each record are calculated just before being written with a SHOW ANALYSIS command sentence or displayed within GRAPH or use (SET) COLOR options followed by IMAGE SET commands to color each atom or residue according to the results of analysis.

See also MAIN_DOC:analysis/analyze.html.

ANALYZE INITIALIZE APPEND ATOMIC RESIDUAL SELECT ... END SET inte SELECT ... END COORDINATES CHARGES RADII TEMPERATURE INTERNAL DISTANCE ANGLE DIHEDRAL ALL ENERGY DISTANCE real RESIDUES int NEIGHBOR int POINTS SURFACE POTENTIAL DENSITY PAIR inte PARAMETER BONDS ANGLES DIHEDRALS IMPROPER

MAP inte STEP inte

... INIT ...

Initializes the analyzes arrays.

... APPEND ...

Analyzed data will be added values already stored in the analysis arrays in contrary to INITIALIZE. APPEND is the default.

... ATOM ...

Analysis records will be organized per ATOM basis. ATOM is the default.

... RESIDUAL ...

Analysis records will be organized per RESIDUE basis. ATOM is the default.

... COORDINATES

Compares the atomic COORDINATES.

... CHARGES

Compares the partial atomic CHARGES.

... RADII

Compares the atomic RADII.

... TEMPERATURE

Compares the TEMPERATURE factors.

... SET inte SELECT ... END

Defines number of records explicitly either directly by an integer number or indirectly through number of SELECTED atoms.

... SELECT ... END ...

SELECTS atoms that are supposed to be analyzed. For syntax see SELECT.

... INTERNAL DISTANCES ANGLES DIHEDRALS

Compares the INTERNAL coordinates: DISTANCE, ANGLES or DIHEDRALS.

... ENERGY DISTANCE real RESIDUES int NEIGHBOR int WHOLE

ANALYZE interaction energies on per atom basis are calculated and stored into analysis arrays for ATOMs or RESIDUEs.

Options enable you to choose part(s) of SELECTION that is within a certain neighborhood criteria: DISTANCE criteria (quality of packing), RESIDUES before and after the chosen atom, through network covalent bond steps (NEIGHBOR), or simply the WHOLE selection.

Interaction energies are calculated on per atom basis for all the ENERGY terms that are currently turned on.

... POINT SURFACE POTENTIAL DENSITY

Analyzes SURFACE, POTENTIAL or density POINT values of SELECTED atoms per ATOM or RESIDUE record as specified above.

The maximum value array contains surface of the whole RESIDUE, when POINTS SURFACE is anaylized in the RESIDUE basis.

... PAIR inte

Divides the whole PAIR list into the specified inte equal parts, and averages the values from the second to the last part in the first one. It works only with the SET flag. The compared distances must be set before by a

MAIN> DEFINE PAIR CALCULATE

statement.

... PARAMETER GENERATE BOND ANGLE DIHEDRAL IMPROPER

Analyzes frequency of appearance and deviation for each particular force field parameter from average value and from its ideal value present in the force. It measures force field reliability and accuracy. PARAMETERS are stored on order of appearance in force field parameter array. ATOM or RESIDUE organization of records has no effect.

GENERATE flag is an option that not only analyzes a kind of an ENERGY term but can also CREATE a new entry in the PARAMETER lists. A useful option for a forcefield creation.

... MAP inte STEP inte

Analyzes the specified MAP by counting its points for a number of intervals specified by STEPS, where each step covers a density interval of the same size, between the map minimal and maximal value. (It creates a HISTOGRAM of a MAP). By writing this data with a SHOW ANALYSIS command sentence, also the portions of each particular interval and their partial sum are being written.

Analysis of temperature factors of the first ten segments. Each segment is supposed to have equal size of atoms.

MAIN> analyze atom init temperature MAIN> analyze set sele numb seg 1 end select segment numb 1 : 10 end

Analysis of PAIR list divided in 5 sets.

MAIN> analyze atom init MAIN> analyze set pair 5 select all end select all end

Analysis of electron density along the chain. First density points are created at each selected atom center.

MAIN> analyze residue init MAIN> analyze poin density sele segment name TRYP end

Analyzes of forcefield parameters (Force field parameters must be read and assigned to atoms.):

MAIN> analyze residue init MAIN> analyze parameter bond sele all end