2007.06.07 -- This application has been archived. Local users, see a CSB staff member for help if you need to run this program in the Core.

ROTAMER

ROTAMER was written by Pat Fleming to answer the following question:
Which side chains in a protein structure are in a defined rotamer conformation and, if in a defined rotamer, is the specific rotamer a major or minor one in terms of occurance?

ROTAMER compares the CHI angle values to the BACKBONE INDEPENDENT rotamer library of Roland Dunbrack as described in Protein Science (1997) 6(8):1661-1681. If the CHI angles for a side chain are within 2 sigma of the respective CHI angle values of a rotamer in that library the residue is considered to be in a rotamer.

ROTAMER requires moleman2 to be available for calculating the CHI angles.

setup rotamer

and

rotamer filename.pdb

The output will be in filename.rot

                 ROTAMER ANALYSIS for 2rns.pdb
 
 Not counting 3 GLY and 10 ALA residues in a total of 116 residues.
 
 66  = NUMBER of residues found in defined rotamer conformations
 64.0777  = PERCENTAGE of non-GLY, non-ALA residues in defined rotamers
 
 To be a DEFINED ROTAMER all the CHI angles must be within +/- 2 sigma of the
   mean angles for that specific rotamer as defined in the rotamer library
   bbind98.Feb.lib of R. Dunbrack, which can be obtained at
   www.fccc.edu/research/labs/dunbrack/bbdep.html.
   [See Protein Science (1997) 6(8):1661-1681.]
 
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 Definitions of the columns in the Table below are:
 
    RES RESNUM - Residue name and number.
 
    ROTAMER - Each CHI is assigned a number 1-4 according to bbind98.Feb.lib
                and this indicates the angle is within 2 sigma of mean value
                for a rotamer of that residue.
              An X marks first CHI that does not fall within 2 sigma of mean
                value for a rotamer of that residue.
              The presence of an X indicates NOT in a defined rotamer.
              A zero indicates that the residue does not have that CHI angle.
 
    PROB - Probability of that ROTAMER for the respective residue.
           The sum of probabilities is 100.0 for each residue.
           Dashes indicate not a defined rotamer.
 
    RANK - MAJOR = Probability of specific rotamer > median probability
                   of all rotamers of that residue.
           minor = Probability of specific rotamer =< median probability
                   of all rotamers of that residue.
           ----- = Not a defined rotamer.
 
    CHI-1  CHI-2  CHI-3  CHI-4 - The value of each angle in degrees.
      [These determined by moleman2 [Kleywegt, (1997)J Mol Biol 273, 371-376]
 
    ROT1 - The angle for CHI-1 falls within the following torsion space.
           (This does not indicate presence or absence of a defined rotamer
             but is useful for consideration of backbone dependence.)
           g+       0 <= CHI-1 < 120
           t      120 <= CHI-1 < 240
           g-    -120 <= CHI-1 <   0
 
    PHI PSI - The value of each angle in degrees.
 
 
RES RESNUM  ROTAMER   PROB  RANK   CHI-1  CHI-2  CHI-3  CHI-4 ROT1  PHI    PSI
-------------------------------------------------------------------------------
LYS      1  2 1 2 X  ----- -----  -156.1   53.2 -152.2  165.9  t  -999.9  156.6
GLU      2  3 2 3 0   9.32 MAJOR   -42.2 -179.8  -73.9  xxxxx  g-  -83.0  140.4
THR      3  1 0 0 0  46.84 MAJOR    64.5  xxxxx  xxxxx  xxxxx  g+  -75.9  168.2
LYS      7  X - - -  ----- -----   177.1  173.1  172.3  -77.1  t   -61.3  -43.3
PHE      8  X - - -  ----- -----   177.6  -88.3  xxxxx  xxxxx  t   -55.5  -47.9
GLU      9  3 2 2 0  16.92 MAJOR   -64.9  163.1  -20.7  xxxxx  g-  -62.6  -43.4
ARG     10  2 X - -  ----- -----   171.3  179.4   59.9   82.6  t   -67.2  -39.2
GLN     11  3 2 3 0  12.02 MAJOR   -65.5 -164.8  -52.9  xxxxx  g-  -78.4  -29.3
HIS     12  3 X - -  ----- -----   -60.3  -64.1  xxxxx  xxxxx  g- -125.5  -13.3
MET     13  3 3 3 0  17.06 MAJOR   -72.1  -55.8  -51.7  xxxxx  g-  -95.8  131.7
ASP     14  2 1 0 0   9.40 MAJOR  -177.8   29.7  xxxxx  xxxxx  t  -150.6   73.7
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