Tool Set Documentation

Jump to: navigation, search


usage: [options] tag
options: [-dir datadir]
         [-prop prop[+prop][,prop]]
         [-cluster tag] [-ctag tag]
         [-score avg|avglow|avgcent|median]
         [-limit low|high|cent]
         [-liminx index]
         [-limstd multiple]
Show source


This script is used for extracting structural properties for a set of structures in an ensemble. It requires a tag as argument to identify the structure set and either one of the options -show or -prop.

The option -prop is used with a comma-separated list of property tags to extract the corresponding data written to standard output. The output consists of data columns in the same order as the tags are given in the list argument. The option -show is available to print the tags for all available properties.

The following tags are commonly available:

etot total energy
eelec electrostatic energy
evdw van der Waals energy
egb Generalized Born energy
esasa Hydrophobic solvation energy
rgyr radius of gyration
rmsdall total RMSD from native
rmsdca C-alpha RMSD from native
rmsdback backbone RMSD from native
rmsdpol polar RMS distance from center
rmsdhyd hydrophobic RMS distance from center
rmsdchg charged RMS distance from center
rmsdphi phi dihed. RMSD from native
rmsdpsi psi dihed. RMSD from native
rmsdchi1 chi1 dihed. RMSD from native
pphi percent correct phi
ppsi percent correct psi
pchi1 percent correct chi1
cont fraction of native contacts
rho fraction of native contacts
gdtts GDT similarity from native

This script only extracts data that has been previously calculated. In order to calculate structural properties for a whole ensemble see Properties may be set from external data with

If the option -score is given a single score is calculated from the property values of all ensemble structures and written out instead of the whole list. The most common use would be to calculate simple averages with -score avg. Values that lie outside a given multiple of the standard deviation can be excluded as in by using avglow or avgcent as key words instead of avg. The option -limstd is available to modify the value of the multiple used in this case.

The option -cluster is available to extract only data for structures in a certain cluster. Clusters can be calculated with If cluster information is only available for a different tag in the same ensemble the tag can be given with -ctag so that the corresponding cluster data is used instead. The -cluster option may be combined with -score to obtain a score for conformations in a given cluster.


usage information
-dir directory 
data directory
print out a list of available properties
-prop prop[+prop][,...] 
list of properties for which data is requested
-cluster tag 
limit output to given cluster
-ctag alttag 
read clustering data from alttag.clusters
-score avg|avglow|avgcent|median 
calculate averages from selected properties
-limstd multiple 
multiple of standard deviation for excluding structures when calculating averages (with -score avglow|avgcent)

Examples -dir data -show sample
prints out the available property tags for structures associated with the sample tag in the ensemble under the data directory

available properties are:
 cont etot gdtts pchi1
 pphi ppsi rgyr rho
 rmsdall rmsdback rmsdca rmsdchg
 rmsdchi1 rmsdhyd rmsdphi rmsdpol
 rmsdpsi -dir data -prop rmsdall,cont sample
extracts total RMSD (rmsdall) and fraction of native contacts (cont) for the sample structures in the ensemble under the data directory

1 13.483227 0.041667 
2 2.994885 0.583333 
3 9.699920 0.125000 
4 9.598882 0.041667 
5 9.066114 0.083333 
6 4.274226 0.500000 
7 2.733985 0.708333 
8 2.774350 0.541667 
9 2.788660 0.708333 -dir data -prop rgyr,cont -cluster t.2 sample
extracts the radius of gyration (rgyr) and fraction of native contacts (cont) for structures in the cluster t.2 associated with the sample tag.

2 9.796450 0.416667 
4 9.306858 0.625000 
5 9.505148 0.708333 
6 9.646953 0.458333 
7 10.014612 0.208333 
9 9.732428 0.583333 
10 12.625645 0.125000 
13 9.622869 0.500000 
14 9.159078 0.708333 
15 9.735043 0.541667 

... -dir data -prop rmsdall,cont -score avg sample
calculates average values for total RMSD and fraction of native contacts

 6.379361 0.370370 -dir data -prop rgyr,cont -score median -cluster t.2 sample
determines median values for the radius of gyration (rgyr) and fraction of native contacts (cont) for structures in the cluster t.2 associated with the sample tag.

 9.735043 0.416667