
Difference between revisions of "Rms.pl"
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chain. Otherwise averages for all chains will be written out.  chain. Otherwise averages for all chains will be written out.  
<BR>  <BR>  
+  
In most cases it is probably desirable to perform a least squares fit between  In most cases it is probably desirable to perform a least squares fit between  
the two structures before calculating root mean square  the two structures before calculating root mean square  
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to all residues outside a subset given with <B>fitx</B>.  to all residues outside a subset given with <B>fitx</B>.  
<BR>  <BR>  
+  
For loop modeling the RMSD calculation can be restricted to a residue  For loop modeling the RMSD calculation can be restricted to a residue  
subset with <B>l</B>. If this option is specified <B>fitxl</B>  subset with <B>l</B>. If this option is specified <B>fitxl</B>  
is available to automatically fit all residues outside the loop or  is available to automatically fit all residues outside the loop or  
fragment.<BR>  fragment.<BR>  
+  
The option <B>nowarn</B> is available for suppressing warnings about  The option <B>nowarn</B> is available for suppressing warnings about  
−  missing atoms. As with  +  missing atoms. As with [[lsqfit.pl]] atoms in the two 
structures are normally matched by atom name, residue name, and  structures are normally matched by atom name, residue name, and  
residue number. This would not allow the comparison of structures with  residue number. This would not allow the comparison of structures with  
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; help : usage information  ; help : usage information  
−  +  ; out cacabconsidebackall... : specify what RMSD value should be printed out  
+  ; detailed : print out a detailed list of different RMSD values  
+  ; chains: calculate RMSD values separately for each chain  
+  ; l min:max[...] : limit RMSD calculation to given range of residues  
+  ; fit : perform leastsquares superposition before calculating RMSD values  
+  ; fitxl : fit structure excluding residue range given with l  
+  ; fitl min:max[...] : fit using specified residue range  
+  ; fitsel cabcacbheavy... : specify which atoms are used for fitting  
+  ; nowarn : do not print out warnings about missing or mismatched atoms  
+  ; resnumonly : match residues based on residue number alone (ignoring residue names)  
+  ; align fasta : provide sequence alignment for comparing two structures with different sequences  
== Examples ==  == Examples == 
Latest revision as of 22:39, 13 September 2010
Usage
usage: rms.pl [options] refPDB cmpPDB options: [out cacabconsidebackall...] [detailed] [chains] [l min:max[...]] [fit] [fitxl] [fitl min:max[...]] [fitx min:max[...]] [fitsel cabcacbheavy] [nowarn] [resnumonly] [useseg] [align fasta]
Description
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
Calpha atoms), cb (Cbeta atoms), cab
(Calpha and Cbeta 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 (Calpha and Cbeta, default),
ca (Calpha), cb (Cbeta), 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
fragment.
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.
Options
 help
 usage information
 out cacabconsidebackall...
 specify what RMSD value should be printed out
 detailed
 print out a detailed list of different RMSD values
 chains
 calculate RMSD values separately for each chain
 l min:max[...]
 limit RMSD calculation to given range of residues
 fit
 perform leastsquares superposition before calculating RMSD values
 fitxl
 fit structure excluding residue range given with l
 fitl min:max[...]
 fit using specified residue range
 fitsel cabcacbheavy...
 specify which atoms are used for fitting
 nowarn
 do not print out warnings about missing or mismatched atoms
 resnumonly
 match residues based on residue number alone (ignoring residue names)
 align fasta
 provide sequence alignment for comparing two structures with different sequences
Examples
rms.pl 1vii.exp.pdb 1vii.exp.min.pdb
calculates the root mean square displacement of all (heavy) atoms
between two structures
1.6750 all
rms.pl out ca fit 1vii.exp.pdb 1vii.exp.min.pdb
calculates the Calpha root mean square diesplacement between two
structures after fitting them with a least squares fit procedure
1.2460 CA
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.
1.5776 all
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 Calpha 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 ...