Pick Item Mode

The mouse can also be used to select things from the screen. As with many molecular graphics programs, an atom can be picked by moving the cursor over it and clicking the left mouse button. When an atom is picked for the first time, a text label appears which shows the atom residue name and number, and the atom name. Clicking on the atom again turns the label off.

Picking atoms with the mouse is used to turn on or off various types of labels, to query for information about an object, or to move items around on the screen. You can label an atom (and display the atom name), or you can label geometric values such as the distance between two atoms (a bond label), an angle between three atoms (an angle label), or the dihedral angle formed by four atoms (a dihedral label). This is done by setting the mouse into the proper picking mode and then selecting the relevant atoms with the mouse.

You first select the proper picking mode by using the Mouse form, and choosing the mode required to perform the desired action. The available actions when in pick item mode are:

• Pick Item Mode $\rightarrow$ Query
  Clicking with the left or middle mouse button on an item will print out the name of the item (e.g. the atom name) to the text console window. The hot key to set this mode is `0'.

• Pick Item Mode $\rightarrow$ Center
  This mode is used to change the point about which a molecule rotates when the molecule is rotated. To cause a molecule to rotate about a specific atom, select this mode and then click on that atom. The rotation point may be restored to its default position (the center of volume of the molecule) by executing the `Reset View' option from the Mouse form. The hot key to set the mouse to Pick Item Mode $\rightarrow$ Centering mode is `c'.

• Pick Item Mode $\rightarrow$ Atom
  Clicking on an atom will toggle on/off a label for the atom. The hot key to set this mode is `1'.

• Pick Item Mode $\rightarrow$ Bond
  Clicking on two atoms in a row will toggle on/off a bond distance label between the two atoms (a dotted line with the distance printed at the midpoint). The hot key to set this mode is `2'.

• Pick Item Mode $\rightarrow$ Angle
  Clicking on three atoms in a row will toggle on/off a label showing the angle formed by the three atoms. The hot key to set this mode is `3'.

• Pick Item Mode $\rightarrow$ Dihedral
  Clicking on four atoms in a row toggles on/off a label showing the dihedral angle formed by the four atoms. The hot key to set this mode is `4'.

• Pick Item Mode $\rightarrow$ MoveAtom
  In this mode, the position of an atom can be changed by clicking on the desired atom, and dragging with the mouse while the button is still pressed. This will change the atom coordinates. The hot key to set this mode is `5'.

• Pick Item Mode $\rightarrow$ MoveResidue
  This mode may be used to move all the atoms in a selected residue at the same time. Select an atom in a residue, and move it to a new position while keeping the mouse button pressed. All the atoms in the same residue as the selected one will be moved the same amount. Holding down the <shift> key and the left mouse button while moving the mouse will rotate the atoms in the residue about the selected atom. If the middle mouse button is held down instead, the atoms in the residue will rotate about a line drawn through the picked atom and parallel to a line coming directly out of the screen. This behavior is similar to the usual Rotate mode, except that coordinates of atoms are changed.

  The hot key to set this mode is `6'.

• Pick Item Mode $\rightarrow$ MoveFragment
  A fragment is a set of atoms all connected by a series of covalent bonds. This mode acts just like MoveResidue, except that the atoms which are moved are all in the selected fragment rather than in the selected residue. This will change the atom coordinates. Holding down the <shift> key and the left mouse button while moving the mouse will rotate the atoms in the fragment about the selected atom. If the middle mouse button is held down instead, the atoms in the fragment will rotate about a line drawn through the picked atom and parallel to a line coming directly out of the screen. This behavior is similar to the usual Rotate mode, except that coordinates of atoms are changed.

  The hot key to set this mode is `7'.

• Pick Item Mode $\rightarrow$ MoveMolecule
  This mode may be used to move all the atoms in a selected molecule at the same time. Select an atom in a molecule, and move it to a new position while keeping the mouse button pressed. All the atoms in the same molecule as the selected one will be moved the same amount. Holding down the <shift> key and the left mouse button while moving the mouse will rotate the atoms in the molecule about the selected atom. If the middle mouse button is held down instead, the atoms in the fragment will rotate about a line drawn through the picked atom and parallel to a line coming directly out of the screen. This behavior is similar to the usual Rotate mode, except that coordinates of atoms are changed.

  The hot key to set this mode is `8'.

When a label is added to a molecule (say, for a bond, or just to show the name of an atom), a new entry will be added to the list of current labels which is available via the Labels form. These controls also contain options to turn the labels on or off, or to delete them entirely from memory.

Fit Submenu

When one has two similar structures, one often wants to compare them. What's the difference between two X-ray structures? How much did the structure change during a simulation? To answer these questions, you must first figure out how to compare two structures, which usually means that you must find the root mean square deviation (RMSD).

Formally, given $N$ atom positions from structure $x$ and the corresponding $N$ atoms from structure $y$ with a weighting factor , the RMSD is defined as:

Using this equation by itself probably won't give you the answer you are looking for. Imagine two identical structures offset by some distance. The RMSD should be 0, but the offset prevents that from happening. What you really want is the minimum RMSD between two given structures; the best fit. There are many ways to do this, but for VMD we have implemented the method of Kabsch (Acta Cryst. (1978) A34, 827-828 or see file Measure.C in the VMD source code). This algorithm computes the transformation, needed to move one structure onto another in order to minimize the RMSD.

With the mathematical prerequisites behind us, we still need to be able to specify how to choose the atoms to compare. If you want to compare all the atoms in both structures, and they both have the same number of atoms, then the problem is easy - $N$ is everything. This occurs most often in MD simulations when the only thing different between two structures are the coordinates.

But what about homologous sequences? In this case, the number of atoms differ because while the number of residues is the same, the sidechains have different numbers of atoms. The usual solution is to determine the RMSD based solely on the backbone atoms or, in some X-ray structures where only the $C_{\alpha}$ atoms have been determined, based on the $C_{\alpha}$ atoms. In addition, VMD allows two other methods for fitting. Fitting by heavy atoms omits the hydrogens, since their positions are often not well determined. Fitting by ``picked atoms'' performs only a translation to bring one atom directly on top of another molecule.

Hopefully the previous discussion revealed the importance of the options available in the fit submenu. Before examining each of them in turn, you should be aware of some VMD definitions. In VMD, a ``molecule'' refers to all the atoms from a structure file. The file may contain multiple molecules under standard chemical usage, but VMD still thinks of them as one molecule. Instead, those individual parts are called ``fragments,'' for lack of a better term. With this said, the fit options in the submenu include:

• Fit $\rightarrow$ Do RMSD Fit
  The fitting will change the stored coordinates of one of the molucules.

• Fit $\rightarrow$ Print RMSD
  VMD wll print out the RMSD between the molecules after fitting them together, without changing their stored coordinates.

• Fit $\rightarrow$ Two Molecules
  
• Fit $\rightarrow$ Two Fragments
  These two submenus contain the same options, which select which atoms of the two molecules should be used to do the least squares fit. For the first submenu, the atoms used will be taken from all the atoms in two different molecules; for the second submenu, the atoms used will only be taken from two separate fragments, where a fragment is a connected chain of residues. The available atom selections for fitting the molecules are:
  • All atoms;
  • Heavy atoms (i.e., all except hydrogen);
  • Backbone atoms;
  • CA (that is, C$_\alpha$) atoms;
  • Picked atoms (i.e., atoms currently labeled on the screen).

  Presently the VMD feedback for RMSD picks is a little terse. To make things clear, here is the process: First select one of the options (i.e., All atoms; Heavy atoms; etc.) from the fit submenu. VMD will respond with a confirmation of your choice and then it will ask you to click on one atom of each of the two selections you would like to compare. The selection you click on first will be moved to the selection you click on second. The atoms that you click on are representative of the entire molecule, fragment, set of heavy atoms, etc. associated with those atoms. Thus, if you have chosen to RMSD fit two molecules, then clicking on one atom for each of the two molecules does in fact specify an RMSD calculation involving all atoms of the two molecules.

  As a simple example of computing RMSD, load the same molecule twice. Press the `8' key (this puts VMD into the ``MoveMolecule'' pick mode and lets you use the mouse to change the coordinates of a molecule). Click and drag one of the molecules away from the other so there is a space between the two.

  By default the fit routines are configured to do the best fit but for this example you will only compute the RMSD, so pick ``Fit $\rightarrow$ Print RMSD.'' Now go to the Mouse form and pick ``Fit $\rightarrow$ Two Molecules $\rightarrow$ All Atoms.'' Look at the VMD console window and you'll see a new line was printed to show the current state. The mouse should look like a crosshair. Pick one of the atoms in the first molecule and then one of the atoms in the second molecule. The value of the RMSD will be printed to the screen, for example:

          RMSD between the two molecules is: 1.123410
  

  In case of two identical molecules the RMSD calculation should, of course, give zero as a result. To stop computing RMSDs, simply change the mouse mode to what you want to do next, for example, press r to go to the rotate mode.

  A discussion of advanced RMSD features available through the scripting interface can be found in section §.

  VMD's atom alignment should be able to handle most common tasks, but there are some it cannot do. If this occurs, you might want to look at Andrew Martin's ProFit at
  http://www.biochem.ucl.ac.uk/~martin/text/ProFit.readme