RIBOSOME

ribosome.py is a program to construct coordinates for a peptide/protein from the amino acid sequence.

Usage: python $LINUS/utils/ribosome.py -p $LINUS/utils/ribosome.dat < [filename].rib > [filename].pdb

where ribosome.dat, is a residue descriptor file. Each residue is described in a Z-matrix style.

All options to the program are passed through a command file [filename].rib. Each command must be given on a separate line. Keywords are case insensitive. All whitespace and tab characters are ignored. All blank lines and lines beginning with a "#" character are ignored. Sample residue descriptor files are given in the Examples section.

FASTA2RIB

fasta2rib.py creates an input file for ribosome.py from an amino acid sequence in FASTA format.

Usage: python $LINUS/utils/fasta2rib.py [filename].fasta

where [filename].fasta is the file containing the sequence in FASTA format. If the file has multiple sequences, only the first sequence is processed.

The output is in a file called [filename].rib.

PDBATOM2FASTA and PDBSEQRES2FASTA

pdbATOM2fasta.py creates a FASTA formatted amino acid sequence file from the ATOM records in a PDB structure file.

pdbSEQRES2fasta.py creates a FASTA formatted amino acid sequence file from the SEQRES records in a PDB structure file.

Usage:
python $LINUS/utils/pdbATOM2fasta.py [filename].pdb

python $LINUS/utils/pdbSEQRES2fasta.py [filename].pdb

where [filename].pdb is a PDB structure file.

The output is [filename].fasta containing the sequence in FASTA format.

VIEWOUT

viewout.py allows one to cycle through the saved structures in the LINUS output file, [filename].out using the molecular graphics program RASMOL.

Usage:
1. In a separate shell window launch RASMOL,
2. Then in the LINUS output directory, enter the command:
python $LINUS/utils/viewout.py [filename].out
3. A menu window will appear that provides choices for the display of the consecutive structures.

TORSION

torsion.py calculates the φ, ψ, ω and all chi angles for a protein structure from a PDB file.

Usage:
python $LINUS/utils/torsion.py pdb[code].ent

The resulting output file, angles.dat, looks like the following:

          SS MS    phi      psi     omega     chi1     chi2
  117 PRO  C P   -89.40    15.89   178.74    35.98   -33.69
  118 ASN  C Q   -87.08    68.06  -176.46   -80.42   -12.81
  119 ASN  T J  -142.64    18.19  -177.29    77.71   136.21
  120 THR  T O   -50.15   -48.72  -176.74   -62.68   999.99
  121 HIS  T J   -97.77    21.09  -178.96   -61.17   -51.21
  122 GLU  H O   -54.79   -49.56  -176.05   179.63   175.71
  123 GLN  H O   -63.61   -43.38   178.65   -70.84   -59.79

with chi angle values extending out as far as necessary to describe a complete side chain conformation.

The SS column indicates the secondary structure using the common H,E,T,C designations for HELIX, EXTENDED, TURN and COIL.

The MS column indicates the mesostate code which is described here.

CONTACT

concnt.py processes the structures written out during a LINUS simulation and lists for each pair of residues the fraction of the structures in which they were in contact. Residues which were never in contact are not listed. The output is written to stdout and consists of 3 columns:

Column 1 - Residue Number
Column 2 - Residue Number
Column 3 - Fraction of structures in which the pair of residues are in contact

Usage:
python $LINUS/utils/concnt.py [filename].pdb [filename].out winmin winmax probe

where:
[filename].pdb = name of pdb file that was input to LINUS simulation
[filename].out = name of file to which sampled structures were written during the course of the simulation
winmin = minimum sequence separation between pairs of residues that are allowed to be in contact
winmax = maximum sequence separation between pairs of residues that are allowed to be in contact
probe = maximum distance between atom surfaces that defines a contact

The resulting output looks like the following:

   4    9 0.030
   4   10 0.010
   9   12 0.060
   9   13 0.040
  10   12 0.090
  10   13 0.050
  10   18 0.020
  12   17 0.060
  12   18 0.010
  13   17 0.090
  13   18 0.010
  17   19 0.260

CHASA

chasa_linus.py estimates the solvation energy of the conformation using the CHASA algorithm. This script is an implementation of the algorithm used on the CHASA webserver (http://roselab.jhu.edu/chasa/) but works with PDB files used in LINUS (which contain unusual atom types). For standard PDB files use either the server or the script which may be downloaded from the server.

Usage:
python $LINUS/utils/chasa_linus.py [linus_type_PDB_file] > chasa.pdb

The resulting output file, chasa.pdb, is a PDB format file which has additional information.

COMPND numintHbd     numSolv    num_nonHbd      total_bb_polar
COMPND     84          147           3              111
.
.
.
ATOM      9  N   THR     2      13.719  19.413  27.573  5.00  0.00
ATOM     10  CA  THR     2      13.088  19.661  26.283  0.00  0.00
ATOM     11  C   THR     2      13.561  18.631  25.300  0.00  0.00
ATOM     12  O   THR     2      14.763  18.432  25.121  3.00  1.57
ATOM     13  CB  THR     2      13.527  20.980  25.667  0.00  7.80
ATOM     14  OG1 THR     2      13.307  22.020  26.627  0.00  5.84
ATOM     15  CG2 THR     2      12.704  21.284  24.409  0.00 16.10
.
.
.
ATOM    149  N   ALA    20       9.346  17.206  29.144  0.00  0.49
ATOM    150  CA  ALA    20       8.985  15.930  29.750  0.00  2.64
ATOM    151  C   ALA    20      10.067  15.607  30.760  0.00  3.52
ATOM    152  O   ALA    20      11.193  16.119  30.686 -1.00  1.77
ATOM    153  CB  ALA    20       8.856  14.815  28.714  0.00  2.39
.
.
.
ATOM    499  O   HOH   120       7.787   1.168  13.283  0.00  0.00
ATOM    500  O   HOH   121       9.368  -0.535   6.166  0.00  0.00
ATOM    501  O   HOH   122      22.918  12.605  15.164  0.00  0.00
ATOM    502  O   HOH   123      16.522  12.543  26.647  0.00  0.00
ATOM    503  O   HOH   124      22.421   8.292  28.255  0.00  0.00
ATOM    504  O   HOH   125      11.087  12.195  10.474  0.00  0.00
TER 1424.592  -52.662

where:

        numintHbd = number of internally hydrogen bonded backbone N and O

        numSolv = number of solvation "waters" (max = 5 per backbone polar group)

        num_nonHbd = number of backbone polar groups not satisfied by hydrogen bonding

        total_bb_polar = number of backbone polar groups in the molecule that should
                         be hydrogen bonded ([2 x Number of residues] -1)

        occupancy column (for N and O only):
            (if > 0.00) = number of solvation "waters" accessible to that atom (max = 5)
            (if = -1.00) = this atom is not hydrogen bond satisfied

        B factor column = CHASA in square angstroms

        TER record:
            (first number) = total CHASA for molecule
            (second number) = solvation free energy for molecule (See below for explanation)

        HOH atoms = solvation "waters" in hydrogen bonding proximity to backbone polar groups
                    (these are the conditional atoms added prior to ASA calculation)

Note 1: The N-terminal nitrogen is not solvated and thus the CHASA value for some atoms proximate to this atom in cartesian space will be standard hydrophobic ASA not conditional hydrophobic ASA.

Note 2: The solvation free energy is calculated as follows:
Total solvation free energy = non-polar + polar solvation free energy, where

Non-polar solvation free energy = total conditional hydrophobic accessible surface area (CHASA) x 0.03
Polar solvation free energy = backbone polar atom solvation free energy, where

Backbone N and O solvation is attempted by placing pseudo water at 5 different postions at appropriate distance and orientation for hydrogen bonding. The number of successfully placed pseudo waters with no steric clash x 0.6 = polar solvation free energy. Backbone oxygens may also be both internally hydrogen bonded AND hydrogen bonded to water. In this case a value of 2.0 is assigned to the solvation free energy of the oxygen.