ACT (CCP4: Supported Program)
NAMEact - analyse coordinates.
SYNOPSISact xyzin xyz_in.pdb
The program always gives statistics for the temperature factors averaged by residue, for the main chain and side chains.
Lists atoms with B-values .gt. bmoni (default = 50).
Lists B-values for Ox1 and Nx2 atoms for each ASN and GLN - if the difference is large the atoms could be wrong way round.
Prints a histogram of solvent molecules in ranges of B-values.
Calculates F000 (the number of electrons in the unit cell).
The optional output includes various contact analyses.
Listing of contacts Keywords: ALL (default) INTERmolecular INTRAmolecular dmin dmax - distance limits for listing contacts, in any order (default = 0.0, 5.0). If only one value given it is assumed to be dmax.
Listing of short contacts
dmoni (default = 2.5) short contacts, up to dmoni, are listed.
Listing of possible hydrogen bonds (by distance criterion) Keywords: ALL (default) INTERmolecular INTRAmolecular hdmin hdmax - distance limits for listing contacts, in any order (default = 2.7, 3.3) A list of unpaired hydrogen bonding atoms is given with HBOND ALL option.
Monitor B-values greater than bmoni (default = 50.0).
Dump ascii plot files (BRES.PLT) for the B-factors to disk
Extract sequence and analyse the amino acid composition.
last card, ends input.
If NAG graphics library is available: Uncomment the call to plotit and the ACTPLOT code and link with the library. You can then plot B-values by residue with keyword:
Plot B-values by residue with NAG graphics library
The program then outputs analysis of the temperature factors by residue for main chain and side chains. For each chain a table is printed for the distribution of residues in ranges of standard deviation of the B-values. The residues with temperature factor greater than three standard deviations from the average value are listed. This analysis is done for main chain and side chain atoms for each chain separately.
A list is given of atoms with B-values grater than bmoni, if input, or 50 by default.
Next follows a list of B-values for the oxygens and nitrogens of the amide groups of glutamines and asparagines. This can be used as a check if those atoms are placed the wrong way round - the difference would then be large.
At the end of the 'compulsory' output a histogram of the solvent moleculs is given in ranges of temperature factors
For the contact searching options pairs of atoms are listed and the distance between then. If the contact is with a symmetry related atom the number of NSYM symmetry operation is given for that atom followed by the number of translations of whole unit cell along x, y and z.
For the HBOND ALL option a list of unpaired hydrogen bonding atoms is given. For well refined structures the atoms with hydrogen bonding potential should normally make a bond, perhaps with the exeption of main chain nitrogens of prolines.
For SEQU option the sequence is extracted from the input file and listed for each chain in both the three-letter and one letter notations. Next the amino acid composition is listed followed by a histogram.
UNIX example script$CEXAM/unix/runnable/act.exam
Example using toxd data.
Example using toxd data.
AUTHORSOriginator : Wojtek Rypniewski and Howard Terry
Contact : firstname.lastname@example.org or email@example.com
SEE ALSOAlternative B factor analysis: