Basic structure calculation starting from given restraints: Difference between revisions

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This calculation shows how to calculate a structure from previously assigned upper limits. The input data are in the subdirectory ‘basic’ of the [[Media:Cyana-3.0-demo.zip|demo data zip archive]]:
This calculation shows how to calculate a structure from previously assigned upper limits and dihedral angle restraints. The input data are in the 'demo/basic' subdirectory of the CYANA software package:


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


 
When CYANA is started, it automatically reads the standard amino acid library and the amino acid sequence of the protein (if multiple sequence files are in the current directory, the most recently modified one is read).  
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''':
The actual structure calculation is performed by the commands in the macro file '''CALC.cya''':

Latest revision as of 08:27, 28 July 2019

This calculation shows how to calculate a structure from previously assigned upper limits and dihedral angle restraints. The input data are in the 'demo/basic' subdirectory of the CYANA software package:

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

When CYANA is started, it automatically reads the standard amino acid library and the amino acid sequence of the protein (if multiple sequence files are in the current directory, the most recently modified one is read).

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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