usage: rms.pl [options] refPDB cmpPDB options: [-out ca|cab|c|o|n|side|back|all...] [-detailed] [-chains] [-l min:max[...]] [-fit] [-fitxl] [-fitl min:max[...]] [-fitx min:max[...]] [-fitsel cab|ca|cb|heavy] [-nowarn] [-resnumonly] [-useseg] [-align fasta]Show source
This script calculates root mean square deviations between two
structures. By default only the total RMSD of all (heavy) atoms is
printed out. Other output modes can be selected with -out.
The following options are recognized: ca (RMSD of
C-alpha atoms), cb (C-beta atoms), cab
(C-alpha and C-beta atoms), c (peptide backbone
carbonyl atoms), o (peptide backbone carbonyl oxygen
atoms), n (peptide backbone nitrogen),
side (side chain heavy atoms), back
(back bone heavy atoms), and all for all (heavy) atoms.
With all of these options only a single value is reported.
Alternatively, a complete set of RMSD values for different atom types,
backbone, sidechains, residue types as well as each residue can be
requested with -detailed. If multiple chains are present, the
option -chains can be used to request RMSD values for each
chain. Otherwise averages for all chains will be written out.
In most cases it is probably desirable to perform a least squares fit between
the two structures before calculating root mean square
deviations. While this is not done by default such a fit can be requested with
-fit. The option -fitsel controls which atoms are used
for the fit. Choices are cab (C-alpha and C-beta, default),
ca (C-alpha), cb (C-beta), and
heavy (all heavy atoms). The least squares fit can
be restricted to a residue subset given with -fitl or
to all residues outside a subset given with -fitx.
For loop modeling the RMSD calculation can be restricted to a residue
subset with -l. If this option is specified -fitxl
is available to automatically fit all residues outside the loop or
The option -nowarn is available for suppressing warnings about missing atoms. As with lsqfit.pl atoms in the two structures are normally matched by atom name, residue name, and residue number. This would not allow the comparison of structures with different amino acid sequences. This is possible when the option -resnumonly is given. In this case, atoms are matched only by atom name and residue number while the residue names are ignored. This is particulary useful for calculating root mean square deviations of backbone atoms between homologous structures. This option also automatically turns off all warnings about missing atoms.
- usage information
- -out ca|cab|c|o|n|side|back|all...
- specify what RMSD value should be printed out
- print out a detailed list of different RMSD values
- calculate RMSD values separately for each chain
- -l min:max[...]
- limit RMSD calculation to given range of residues
- perform least-squares superposition before calculating RMSD values
- fit structure excluding residue range given with -l
- -fitl min:max[...]
- fit using specified residue range
- -fitsel cab|ca|cb|heavy...
- specify which atoms are used for fitting
- do not print out warnings about missing or mismatched atoms
- match residues based on residue number alone (ignoring residue names)
- -align fasta
- provide sequence alignment for comparing two structures with different sequences
rms.pl 1vii.exp.pdb 1vii.exp.min.pdb
calculates the root mean square displacement of all (heavy) atoms between two structures
rms.pl -out ca -fit 1vii.exp.pdb 1vii.exp.min.pdb
calculates the C-alpha root mean square diesplacement between two structures after fitting them with a least squares fit procedure
rms.pl -l 10:21 -fitxl 1vii.exp.pdb 1vii.exp.min.pdb
calculates the root mean square displacement for residues 10 through 21 between two structures. The structures are fitted with a least squares procedure of all residues outside the range for which the RMSD is calculated. This is a typical example for comparing loop structures.
rms.pl -detailed -l 10:15 -fitl 10:21 -fitsel ca 1vii.exp.pdb 1vii.exp.min.pdb
calculates the root mean square displacement for residues 10 through 15 between two structures after least squares fitting C-alpha atoms of residues 10 through 21. The detailed output contains RMSD values for each residue, residue type, and specific atom subsets.
all 1.5541 back 1.0124 CA 0.9523 N 0.6613 C 0.8758 O 1.4102 side 1.9508 CAB 1.2323 CB 1.5009 ARG 1.7635 ...