VMD

Useful commands and features of the powerfull VMD software (Humphrey, W., Dalke, A. and Schulten, K., "VMD - Visual Molecular Dynamics", J. Molec. Graphics, 1996, vol. 14, pp. 33-38.)

http://www.ks.uiuc.edu/Research/vmd/

Start vmd

 * type vmd in a shell.
 * Read in pdb or xyz file directly: vmd pdb_name.pdb or vmd xyz_name.xyz

Select atoms/residues
After starting a VMD shell (see above) go to
 * Graphics => Representations: The menu "Selected Atoms" can be used
 * name FE selects iron atoms
 * name CA (typically selects alpha-C in protiens if the "normal" pdb name for alpha carbons are used)
 * within 5 of name FE (selects all atoms withn 5 Å of FE)
 * resname CYS (selects cystein residues)

More on selecting atoms
For saving a pdb selction, open vmd

1) load the pdb file

mol new pdb.pdb

2) Example 1: Select all:

set sel1 [atomselect top "all"]

Check that the number of atoms fit

$sel1num

3) Selection of atoms within 5 Å of another atom (here "Mn")

vmd > set sel2 [atomselect top "within 5 of name MN"]

4) Select whole molecules (here waters - and only waters)

vmd > set sel3 [atomselect top "same residue as (water within 5 of name MN)"]

5) First residues and waters within 5 Å)

vmd > set sel3 [atomselect top "resid 1 or (same residue as (water within 5 of resid 1))"]

6) writing using writepdb selection:

vmd > $selX writepdb pdb_out.pdb

Align molecules with RMSD Tool
After starting a VMD shell (see above) go to
 * Extensions => Analysis => RMSD Trajectory Tool. Check that it is the right molecules that are read in (try "Add all"). Now type for the atoms that should be aligned (in box upper left)
 * name ATOM1 ATOM2 ATOM3 etc. (note that they should have the same name in the pdb/xyz files that are compared. It only works if there are equally many of the atom types in the fwo files!). Press "ALIGN". IMPORTANT: The align will happend according to the "top" molecule (marked with "T" in the VMD main window - this molecule will have unchanged coordinates)
 * xyz or pdb file can be written out with from File => Save Coordinates.