Basic structure calculation starting from given restraints: Difference between revisions

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When CYANA is started, it automatically executes the commands in the initialization macro file '''init.cya''', which usually holds basic setup for the calculations, e.g., reading the amino acid library and the amino acid sequence of the protein, and specifying general parameters such as the residue range for RMSD calculations. These commands could be put into the '''CALC.cya''' macro file (or even given on the command line), but as they are rarely changed for a given project, it is convenient have them in the '''init.cya''' file:
When CYANA is started, it automatically executes the commands in the initialization macro file '''init.cya''', which usually holds basic setup for the calculations, e.g., reading the amino acid library and the amino acid sequence of the protein, and specifying general parameters such as the residue range for RMSD calculations. These commands could be put into the '''CALC.cya''' macro file (or even given on the command line), but as they are rarely changed for a given project, it is convenient have them in the '''init.cya''' file:


  rmsdrange:=10-100                    # define residue range for RMSD calculations
rmsdrange:=10-100                    # define residue range for RMSD calculations
  cyanalib                              # read standard CYANA residue library  
cyanalib                              # read standard CYANA residue library  
  read seq demo.seq                    # read amino acid sequence
read seq demo.seq                    # read amino acid sequence


The actual structure calculation is performed by the commands in the macro file '''CALC.cya''':
The actual structure calculation is performed by the commands in the macro file '''CALC.cya''':


  read upl demo.upl # read upper distance bounds
read upl demo.upl # read upper distance bounds
  read aco demo.aco # read dihedral angle restraints
read aco demo.aco # read dihedral angle restraints
 
  calc_all 50 steps=4000 # calculate conformers
calc_all 50 steps=4000 # calculate conformers
 
  overview demo.ovw structures=10 pdb # analyze and write best conformers
overview demo.ovw structures=10 pdb # analyze and write best conformers


[[Image:StructuresDemoBasic.png|thumb|200px|'''demo.pdb'''.]]
[[Image:StructuresDemoBasic.png|thumb|200px|'''demo.pdb'''.]]
The first two commands read the input files with upper distance bounds and dihedral angle restraints, respectively. Then, 50 conformers are calculated using the standard [[simulated annealing]] schedule with 4000 [[torsion angle dynamics]] steps per conformer. Finally, the 10 conformers with the lowest final target function values are analyzed. The coordinates of these 10 best conformers are written to the PDB file '''demo.pdb''', and an overview table is saved in the file '''demo.ovw''':
The first two commands read the input files with upper distance bounds and dihedral angle restraints, respectively. Then, 50 conformers are calculated using the standard [[simulated annealing]] schedule with 4000 [[torsion angle dynamics]] steps per conformer. Finally, the 10 conformers with the lowest final target function values are analyzed. The coordinates of these 10 best conformers are written to the PDB file '''demo.pdb''', and an overview table is saved in the file '''demo.ovw''':
   
   
    Structural statistics:
  Structural statistics:
 
    str  target    upper limits    van der Waals  torsion angles
  str  target    upper limits    van der Waals  torsion angles
        function  #    rms  max  #    sum  max  #    rms  max
      function  #    rms  max  #    sum  max  #    rms  max
      1    1.56  1 0.0073  0.36  5    5.2  0.34  0 0.3460  3.19
    1    1.56  1 0.0073  0.36  5    5.2  0.34  0 0.3460  3.19
      2    1.87  2 0.0084  0.36  5    6.1  0.33  0 0.3813  3.63
    2    1.87  2 0.0084  0.36  5    6.1  0.33  0 0.3813  3.63
      3    1.92  2 0.0083  0.36  5    5.8  0.36  0 0.3491  3.29
    3    1.92  2 0.0083  0.36  5    5.8  0.36  0 0.3491  3.29
      4    1.94  1 0.0082  0.36  6    6.4  0.34  0 0.3478  3.46
    4    1.94  1 0.0082  0.36  6    6.4  0.34  0 0.3478  3.46
      5    2.02  2 0.0080  0.35  7    5.7  0.34  0 0.5790  4.35
    5    2.02  2 0.0080  0.35  7    5.7  0.34  0 0.5790  4.35
      6    2.05  1 0.0082  0.35  8    6.0  0.34  0 0.5704  4.29
    6    2.05  1 0.0082  0.35  8    6.0  0.34  0 0.5704  4.29
      7    2.12  2 0.0092  0.36  4    6.5  0.35  0 0.3629  3.47
    7    2.12  2 0.0092  0.36  4    6.5  0.35  0 0.3629  3.47
      8    2.20  4 0.0105  0.36  5    7.2  0.31  0 0.3597  3.45
    8    2.20  4 0.0105  0.36  5    7.2  0.31  0 0.3597  3.45
      9    2.24  2 0.0087  0.36  6    7.4  0.34  0 0.3843  3.47
    9    2.24  2 0.0087  0.36  6    7.4  0.34  0 0.3843  3.47
    10    2.34  3 0.0119  0.61  5    6.6  0.35  0 0.3309  3.05
  10    2.34  3 0.0119  0.61  5    6.6  0.35  0 0.3309  3.05
   
   
    Ave    2.03  2 0.0089  0.38  6    6.3  0.34  0 0.4011  3.56
  Ave    2.03  2 0.0089  0.38  6    6.3  0.34  0 0.4011  3.56
    +/-    0.21  1 0.0013  0.08  1    0.7  0.01  0 0.0881  0.41
  +/-    0.21  1 0.0013  0.08  1    0.7  0.01  0 0.0881  0.41
    Min    1.56  1 0.0073  0.35  4    5.2  0.31  0 0.3309  3.05
  Min    1.56  1 0.0073  0.35  4    5.2  0.31  0 0.3309  3.05
    Max    2.34  4 0.0119  0.61  8    7.4  0.36  0 0.5790  4.35
  Max    2.34  4 0.0119  0.61  8    7.4  0.36  0 0.5790  4.35
    Cut                      0.20            0.20            5.00
  Cut                      0.20            0.20            5.00
   
   
    Constraints violated in 3 or more structures:
  Constraints violated in 3 or more structures:
                                                  #  mean  max.  1  5  10
                                                #  mean  max.  1  5  10
    Upper HA    ASP  68 - H    ASN  69  3.28  4  0.11  0.29  +*  ++    peak 1162
  Upper HA    ASP  68 - H    ASN  69  3.28  4  0.11  0.29  +*  ++    peak 1162
    Upper HB    ILE  85 - H    ASP  86  3.80  10  0.36  0.36  +++++++++*  peak 803
  Upper HB    ILE  85 - H    ASP  86  3.80  10  0.36  0.36  +++++++++*  peak 803
    VdW  N    LEU  39 - CD1  LEU  39  3.05  10  0.23  0.24  ++++++++*+
  VdW  N    LEU  39 - CD1  LEU  39  3.05  10  0.23  0.24  ++++++++*+
    VdW  N    ILE  81 - CD    PRO  82  3.05  10  0.26  0.28  ++*+++++++
  VdW  N    ILE  81 - CD    PRO  82  3.05  10  0.26  0.28  ++*+++++++
    VdW  N    ILE  81 - HD2  PRO  82  2.45  10  0.34  0.36  ++*+++++++
  VdW  N    ILE  81 - HD2  PRO  82  2.45  10  0.34  0.36  ++*+++++++
    VdW  CG2  ILE  81 - C    ILE  81  2.90  6  0.20  0.22  ++  ++ *+
  VdW  CG2  ILE  81 - C    ILE  81  2.90  6  0.20  0.22  ++  ++ *+
    VdW  CB    THR  91 - H    GLN  92  2.55  7  0.22  0.27  ++++++  *
  VdW  CB    THR  91 - H    GLN  92  2.55  7  0.22  0.27  ++++++  *
    VdW  O    THR  91 - CB    GLN  92  2.90  3  0.15  0.20      * ++
  VdW  O    THR  91 - CB    GLN  92  2.90  3  0.15  0.20      * ++
    VdW  HA    VAL  107 - CD    PRO  108  2.60  4  0.18  0.30    *+  + +
  VdW  HA    VAL  107 - CD    PRO  108  2.60  4  0.18  0.30    *+  + +
    2 violated distance restraints.
  2 violated distance restraints.
    7 violated van der Waals restraints.
  7 violated van der Waals restraints.
    0 violated angle restraints.
  0 violated angle restraints.
   
   
    RMSDs for residues 10..100:
  RMSDs for residues 10..100:
    Average backbone RMSD to mean  :    0.52 +/- 0.09 A (0.40..0.72 A; 10 structures)
  Average backbone RMSD to mean  :    0.52 +/- 0.09 A (0.40..0.72 A; 10 structures)
    Average heavy atom RMSD to mean :    1.04 +/- 0.06 A (0.96..1.17 A; 10 structures)
  Average heavy atom RMSD to mean :    1.04 +/- 0.06 A (0.96..1.17 A; 10 structures)

Revision as of 14:23, 2 June 2009

This calculation shows how to calculate a structure from previously assigned upper limits. The input data are in the subdirectory ‘basic’ of the demo data zip archive:

demo.seq
amino acid sequence
demo.upl
upper distance limit restraints
demo.aco
dihedral angle restraints
init.cya
initialization macro
CALC.cya
macro for the structure calculation


When CYANA is started, it automatically executes the commands in the initialization macro file init.cya, which usually holds basic setup for the calculations, e.g., reading the amino acid library and the amino acid sequence of the protein, and specifying general parameters such as the residue range for RMSD calculations. These commands could be put into the CALC.cya macro file (or even given on the command line), but as they are rarely changed for a given project, it is convenient have them in the init.cya file: 

rmsdrange:=10-100                     # define residue range for RMSD calculations
cyanalib                              # read standard CYANA residue library 
read seq demo.seq                     # read amino acid sequence

The actual structure calculation is performed by the commands in the macro file CALC.cya: 

read upl demo.upl			# read upper distance bounds
read aco demo.aco			# read dihedral angle restraints

calc_all 50 steps=4000		# calculate conformers

overview demo.ovw structures=10 pdb	# analyze and write best conformers
demo.pdb.

The first two commands read the input files with upper distance bounds and dihedral angle restraints, respectively. Then, 50 conformers are calculated using the standard simulated annealing schedule with 4000 torsion angle dynamics steps per conformer. Finally, the 10 conformers with the lowest final target function values are analyzed. The coordinates of these 10 best conformers are written to the PDB file demo.pdb, and an overview table is saved in the file demo.ovw: 

 Structural statistics:
 
 str   target     upper limits    van der Waals   torsion angles
     function   #    rms   max   #    sum   max   #    rms   max
   1     1.56   1 0.0073  0.36   5    5.2  0.34   0 0.3460  3.19
   2     1.87   2 0.0084  0.36   5    6.1  0.33   0 0.3813  3.63
   3     1.92   2 0.0083  0.36   5    5.8  0.36   0 0.3491  3.29
   4     1.94   1 0.0082  0.36   6    6.4  0.34   0 0.3478  3.46
   5     2.02   2 0.0080  0.35   7    5.7  0.34   0 0.5790  4.35
   6     2.05   1 0.0082  0.35   8    6.0  0.34   0 0.5704  4.29
   7     2.12   2 0.0092  0.36   4    6.5  0.35   0 0.3629  3.47
   8     2.20   4 0.0105  0.36   5    7.2  0.31   0 0.3597  3.45
   9     2.24   2 0.0087  0.36   6    7.4  0.34   0 0.3843  3.47
  10     2.34   3 0.0119  0.61   5    6.6  0.35   0 0.3309  3.05

 Ave     2.03   2 0.0089  0.38   6    6.3  0.34   0 0.4011  3.56
 +/-     0.21   1 0.0013  0.08   1    0.7  0.01   0 0.0881  0.41
 Min     1.56   1 0.0073  0.35   4    5.2  0.31   0 0.3309  3.05
 Max     2.34   4 0.0119  0.61   8    7.4  0.36   0 0.5790  4.35
 Cut                      0.20             0.20             5.00

 Constraints violated in 3 or more structures:
                                                #   mean   max.  1   5   10
 Upper HA    ASP   68 - H     ASN   69   3.28   4   0.11   0.29   +*   ++    peak 1162
 Upper HB    ILE   85 - H     ASP   86   3.80  10   0.36   0.36  +++++++++*  peak 803
 VdW   N     LEU   39 - CD1   LEU   39   3.05  10   0.23   0.24  ++++++++*+
 VdW   N     ILE   81 - CD    PRO   82   3.05  10   0.26   0.28  ++*+++++++
 VdW   N     ILE   81 - HD2   PRO   82   2.45  10   0.34   0.36  ++*+++++++
 VdW   CG2   ILE   81 - C     ILE   81   2.90   6   0.20   0.22  ++  ++ *+
 VdW   CB    THR   91 - H     GLN   92   2.55   7   0.22   0.27  ++++++   *
 VdW   O     THR   91 - CB    GLN   92   2.90   3   0.15   0.20       * ++
 VdW   HA    VAL  107 - CD    PRO  108   2.60   4   0.18   0.30    *+  + +
 2 violated distance restraints.
 7 violated van der Waals restraints.
 0 violated angle restraints.

 RMSDs for residues 10..100:
 Average backbone RMSD to mean   :    0.52 +/- 0.09 A (0.40..0.72 A; 10 structures)
 Average heavy atom RMSD to mean :    1.04 +/- 0.06 A (0.96..1.17 A; 10 structures)
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