A TCL VMD Program for the easy and flexible trajectory analysis.

  ANJI BABU KAPAKAYLA
  IIT KANPUR, INDIA.
  [email protected]

  source ECT.tcl in VMD tk console

 my_commnds: Prints available commands on the console
 Alignment, RMSD ,distance, angle, dihedral, contact_map
 clustering, details, count_waters, HBonds, pbs_box, 
 save_pdb, save_image, sasa, save_coordinates, bgcolor
 HB_occupancy, show_interactions, show_hbonds,count_hbonds
 --help

 my_commands   : Shows all available commands

  Gives details of any mentioned command
  USAGE   : --help command
  example : --help distance
  example : --help angle

  Writes pdb file for given options
  USAGE : save_pdb atomselection start_frame end_frame stride molid filename
  EXAMPLE  : save_pdb "protein" 5 100 5 top file.pdb
  Above example , It will write file.pdb for "protein" from frame 5 to 100 by skipping every 5 frames.

  align molid1 molid2
  example   : align 0 1

  Measures Avg.RMSD & std for given selections
  USAGE    : rmsd Atomselection molid1  molid2
  example  : rmsd "backbone" top  1
  example  : rmsd "protein" top top
  IF both the molids are same , RMSD will be calculated by taking zeroth frame as reference

  Measures Distance, Avg Distance & std for any given 2 atoms
  USAGE    : distance sel1 sel2 <initial-frame> <end-frame> <-show_plot>
  example  : distance "serial 3418" "serial 3415" 
  example  : distance "serial 3418" "serial 3415" 100 2000
  example  : distance "serial 3418" "serial 3415" -show_plot
  example  : distance "serial 3418" "serial 3415" 10 1000 -show_plot
  OUTPUT   : DISTANCE.xvg and dist.png

  Measures Avg. angle & std  for any given 3 atoms
  USAGE    : angle sel1 sel2 sel3
  example  : angle "serial 3418" "serial 3415" "serial 3395"
  OUTPUT   : ANGLE.dat

  Measures Avg Dihedral angle & std  for any given 4 atoms 
  USAGE    : dihedral sel1 sel2 sel3 sel4
  example  : dihedral "serial 3418" "serial 3415" "serial 3412" "serial 3395"
  example2 : dihedral "index 3417" "index 3414" "index 3411" "index 3394"
  OUTPUT   : DIHEDRAL.dat

  Prints RESID and corresponding RESNAME for given selection and for given frames
  USAGE    : show_residues sel molid <initial frame>  <final frame>
  example  : show_residues "resid 170 to 180" 0 0 5
  example2 : show_residues "(not resname WAT) and within 3 of resid 235" 0 5 10
  example3 : show_residues "protein and hydrophobic " 0 1 0
  OUTPUT   : RESNAMES.dat

  Prints required molecular details for given molid
  USAGE    : details molid
  example  : details 0

  Prints Avg. No of waters present around given selection
  USAGE    : count_waters sel molid start_frame end_frame
  Example  : count_waters "within 5 of resid 235" 0 5 10
  OUTPUT   : NO-OF-WATERS.dat