RMSDTT: RMSD Trajectory Tool v2.0

Options

• Menu:
  • File: the RMSD values can be plotted or saved to file after the calculation (options Save data and Plot data) or during the calculation (through plot and save to file options in the main window). Do not change the trajectory options in the main window for this to work (except the Time options, which can be changed). Save summary will save the summary of the data as it appears in the table to file.
  • The Options menu allows you to select different programs for plotting, to change the definition of the backbone, switch on/off the output of statistics, and color the table by molecule number (the table will only be colored if this switch in on and the plot option is on during the calculation).
• Atoms selection:
  • Multi-line atoms selection box. The selection can be split in different lines. The character '#' can be used to comment out a portion of the selection, namely from the '#' to the end of that line (see figure above).
  • trace will add 'and name CA' to the atoms selection.
  • backbone will add 'and name C CA N' (default) or 'and name C CA N O' to the atoms selection. The backbone definition to use can be choose from menu (Options | Backbone def...).
  • noh will exclude hydrogens from the atoms selection (adds 'and noh' to the atoms selection).
  • history is a drop down menu of previously used selections. It is updated when pressing RMSD (not anymore by pressing Return).
• Swapping atoms:
  • Swap_atoms will try to swap equivalent atoms to reduce the RMSD value. Sets of equivalent atoms can be selected from the drop down menu (defaults to All defined pairs). How to define or delete new pairs is explained in the Swap plugin webpage. You need to have the Swap plugin installed to see this options. It does not work with Align.
  • The verbose option will print the out the status of the swapped atoms during the RMSD calculations.
  • The List button will print out the current definitions.
• Calculation type:
  • RMSD will calculate the RMSD using the reference molecule defined in Ref and the structures in the table as targets. Note that the RMSD button has to be pressed again to obtain the new RMSD values after the alignment.
  • Align will align the structures in the table using the molecule defined in Ref as reference. Align is not available if the All in the trajectory options is active or Average is used as reference.
• Reference molecule:
  • Top will use the actual top molecule as reference (it doesn't need to be one included in the table).
  • Average will use the average structure calculated from all the molecules in the table (and all frames if trajectory is activated) as reference. It does not work for Align calculations.
  • Selected will use the molecule selected in the table as reference. If more than one molecule is selected, only the first one will be used as reference.
• Trajectory options:
  • Trajectory activates options to include the frames of a molecule in the calculations.
  • Frame ref sets the frame of reference for the reference molecule. if the reference molecule is set to Average, all frames are used.
  • All activates the calculation of the RMSD of all frames in the selected structures against all frames in the reference molecule.
  • Skip allows to skip frames in a regular fashion, starting from Start and skipping every Steps.
  • Time activates the use of time units. Ini is the initial time, and Step is the time between frames. This changes will be reflected in the plot and the output file.
  • Plot will use the Multiplot VMD plugin (available in all systems), Xmgrace (only on unix) or MS Excel (only windows) to plot the data RMSD vs frame/time. This options is not available if the All option is on. The same plot can be obtained from the File menu. Xmgrace or MS Excel have to be installed on the system by the user. MS Excel needs the tcom tcl library (see installation instructions). VMD gives a warning message when exiting on windows systems if MS Excel is open with data from VMD, but you still can continue using MS Excel.
  • Save to file will save the data to the specified file. The format of the data depends on the status of the All option. If it is off, the format is a table in which each row represents a frame and each column a molecule or trajectory. If All is on, the data is a table in which each row represents the RMSD between the corresponding ref_mol/ref_frame and target_mol/target_frame pairs. If the trajectories have differing numbers of frames, NA (not available) is used. The data can also be saved from the File menu.

    All off		All on
    frame mol 1 mol 2 mol 3 0 0.652 2.828 0.652 1 NA NA 0.659 2 NA NA 0.674 3 NA NA 0.692 4 NA NA 0.722 5 NA NA 0.743 ... ... ... ...		ref_mol ref_frame mol frame rmsd 0 0 1 0 0.652 0 0 2 0 2.828 0 0 3 0 0.652 0 0 3 1 0.659 0 0 3 2 0.674 0 0 3 3 0.692 ... ... ... ... ...

• Table of target molecules: This table shows the results by molecule. It presents the average, standard deviation, minimum, maximum and number of frames used (this number does not need to be the same as the number of frames in the molecule, since the reference molecule/frame is not included in the calculation). The Overall row shows the overall values as if all frames were independent of each other, i. e., it is not an average of the averages.

  The following buttons can be used to add/remove molecules from the table:

  • Erase all deletes all molecules from the list.
  • Erase selected deletes the selected molecule from the list.
  • Add all adds all molecules to the list.
  • Add active adds only the active molecules to the list.