SymD (Symmetry Detection)
SymD version 1.61 can handle multi-chain structures with up to 12000 residues. It includes several options where users can specify by the following command:
symd -options name.pdb
Options are separated by one or more spaces. There can be any number of options and the order is immaterial. Each option starts with a minus sign (‘-‘) in order to distinguish it from the file name field. Following options are recognized by the current version:
-is [num] Initial shift value.
Default is all possible values], from –(nres-3) to +(nres – 3). When this option is given, only the specified initial shift will be tried.
-mxna [num] Maximum number of atoms. Must be > 3. Default = 10,000.
-nopermute Do not permute the structure.
-nofsd Do not use “floating seeds”. “Floating seeds” are seed pairs that have ties. SE routine do not use these pairs as seeds, but normally adds them among the aligned pairs at the end. However, when the nofsd option is given, these are ignored.
-norefine Do not do RSE refinement of the initial alignment.
-pivot [num] T-score is calculated as T=Sum(1/[1+(d/d0)^n]).
-slope [num] Pivot is d0 and slope is n in above formula. Default: d0 = 2.0; n = 2.
-selcon If this option is not given, RSE always does 10 cycles of refinement. With this option, RSE terminates if alignment converges before then.
-mina [num] Minimum angle in degrees used in symmetry axis calculation. If the rotation angle determined from the transformation matrix is less than this value, then the symmetry operation is considered as pure translation, in which case the symmetry axis is placed to pass through the center of mass of the molecule. Default = 2.0 degrees.
-mp Monitor the progress.
-complete Produce a “complete” output. Default: produce a “simple” output.
-fasta Produce FASTA format alignment output file.
-sia Show initial alignment.
-sfa Show final alignment.
-sis Save transformed structure after the initial alignment.
-sfs Save transformed structure after the final alignment.
-sos Include the original structure in the transformed structure output.
-bkt Output details of clustering the high z-score points.
-axisLen [num] Half axis length in A. Default: radius of gyration of the molecule.
The SymD1.61 executables for Mac and Linux as well as sample results can be download.
mAxesD runs on Mac OS X 10.5 or later. It takes the info.txt output from SymD as the input and output the multiple (if any) symmetry axes information including initial shift, TM-score, Z-score and rotation angle.