Q.813 - How can I calculate/plot RMS distances between structures ?

Use RMSPDB. From the manual:

You have some flexibility in selecting which residues and atoms should be compared:

• - you may choose to compare a single chain or any/all chains by providing a 2-character chain identifier in the first case (e.g., "S2" or " A"), or by typing "**" in the latter

• - you may allow for homology, which will cause the program to ignore the residue NAMES (when it looks for counterparts of atoms from the first file), but NOT the residue NUMBERS

• - as for the residues, you may compare all residues, or just a range (use the latter option, for example to compare just the protein, but not the ligands, solvent molecules, salt ions etc.). Alternatively, you may supply several ranges of residue numbers to use or exclude (e.g., when you compare two homologous but not identical proteins)

• - as for atoms, you may compare all atoms, just the C-alpha atoms, just the main-chain atoms (N, CA, C, O) or all non-main-chain atoms (i.e., including solvent etc.). Alternatively, you may enter the names of atoms which you want to compare or to exclude explicitly. Note that the second and third option imply that only amino-acid residues are compared !

Optionally, you may produce plot output files which can be viewed with O2D and turned into PostScript files by the same program. In that case, you must provide the following information:

• - name of the three plot files (one for the atom-by-atom distances, one for the average per-residue distance and one for a histogram of distances

• - the number of intervals in your histogram plot plus the values at the interval boundaries (i.e., one value more than thee number of intervals ...)

• - whether you want the atoms and residues in the plot files to be numbered consecutively (i.e., 1, 2, ...) or explicitly (for atoms: the number of the atom in the first PDB file; for residues: the actual residue number)

The output consists of information regarding the differences in X-, Y- and Z-coordinates, occupancy factors and individual isotropic temperature factors as well as information about the total, average and RMS positional shifts (i.e., combining X-, Y- and Z-shifts).

You may then go back to any part of the input stage, to run the program for different residues, atom types or even files, or quit the program.

Use this program, for example, to compare two different models of your protein, to compare your protein with and without ligand, to get quantitative information about the effect of a cycle of X-PLOR or PROLSQ refinement, to compare your structure with someone else's XRAY or NMR structure, etc.

The (optional) plot files are ASCII files suitable for O2D. See the O2D manual for information about the keywords. You may for example want to change the colour of the plots or the viewport (in particular, when you want to compare a number of plots on the same scale). O2D can create PostScript files which you may subsequently view or plot.

NOTE: LSQMAN is the preferred program nowadays.