Calculating RMSDs

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The ability to calculate RMSDs in PLOP is provided as a convenience. Please note that it is only intended to compare structures with identical sequences (or at the very least, only minimally different, such as a few missing residues at the termini). It tries to be tolerant of differences in residue numbering, but there are limits. If you want to compare proteins with different sequences, use one of the many "structure alignment" programs out there.

These caveats aside, the RMSD command provides a great deal of flexibility in defining which atoms should be aligned, and which atoms to calculate the RMSD over. This is a critical distinction, sometimes ignored in other programs. You might, for example, want to align the backbone for the entire protein, but then measure the RMSD over a few side chains that are known to constitute an active site. This is different from aligning the side chains themselves (which might cause the backbones to be grossly misaligned).

The general syntax is

 rmsd external file &
   align type residue selection &
   rmsd type residue selection

where "file" is some PDB file with a sequence identical to the protein currently in memory, "align" specifies which atoms to align, and "rmsd" specifies which atoms to calculate the RMSD over. The "residue selection" syntax is described above. But in addition to specifying which residues, you may want to specify only some subset ("type") of atoms in the residues to include in the calculation. The current options include "calpha" (just C-alpha atoms), "back" (N, C-alpha, C), "side" (all side chain heavy atoms), or, if you do want all (heavy) atoms in the residues, then use "res[idues]".

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