suppose - superposition of multiple structures
USAGE
suppose [-mat] [-rot] [-mean] [-sd] [-cmp <cmppdb>] [-fit
<fitexpr>] [-calc <calcexpr>] [-pr <atomlist>] <pdb-files>
DESCRIPTION
This is a program written in the NAB molecular manipula-
tion lanuguage (http://www.scripps.edu/case/casegroup-
sh-2.2.html#sh-2.2) to supercede Bob Diamond's multiple
superposition program, "superpose". It overcomes a number
of superpose's limitations and undocumented bugs while
retaining its functionality as well as adding features
and improving some aspects of it, particularly the way
atom selections are made for defining regions of the
molecule you wish to superimpose and get statistics for.
suppose takes structures as pdb files and fits each struc-
ture onto every other, computing the fitting error for
each pair and optionally, for each residue of each
pair. It then uses this complete set of pairwise rms
deviations to compute the overall rms pairwise deviation
between structures.
suppose also computes the mean structure by superimposing
all structures onto the first one and then averaging each
coordinate of each atom over all the molecules. It then
determines the deviation of each structure from this mean
coordinate set and reports the overall rms deviation from
the mean. The deviation of each structure and overall
rms deviation from a user-specified coordinate set can
also be obtained by using the -cmp option (i.e. to compare
an NMR family to an Xray structure). The program can then
write the set of fitted, rotated coordinates and/or the
mean structure back as new pdb files. All input files
must have the same atoms in the same order.
OPTIONS
-mat will write to STDOUT a matrix of all pairwise devia-
tions as well as a table containing the deviation
of each structure from the mean and optionally,
from an arbitrary input structure (see the -cmp
options for details).
-rot will write out fitted, rotated coordinates to files
with ".rot.pdb" in place of the last extension of
the input file names. For example, if you speci-
fied *.pdb as the input files, the rotated files
would be called *.rot.pdb.
-mean will cause the mean structure (after superposition)
RMS values. I'm not sure error bars on an RMSD are
very meaningful, but people have asked for it...
-cmp <cmppdb>
indicates that each of the input structures should
be compared to <cmppdb> similar to the way each one
gets compared to the mean structure. Overall RMS
from <cmppdb> and optionally (via -mat), the RMSD
from each structure is reported. This could be
useful for comparing an NMR family to an Xray or
some other Brookhaven structure, for example. The
-rot option will cause <cmppdb> to be fitted and
written out along with the input files. Note that
<cmppdb> must be the same molecule as the input
structures with the atoms in the same order!
-fit <"fitexpr">
indicates that the atoms to be used in the various
fits will be specified by the NAB atom expression
<fitexpr>. See below. Default is all atoms. It is
recommended that <fitexpr> be contained in quotes.
-calc <"calcexpr">
indicates the atoms to be used in calculating rms
differences will be specified by the NAB atom
expression <calcexpr> after the fit. See below.
Default is all atoms. It is recommended that <cal-
cexpr> be contained in quotes.
-pr <"atomlist">
causes suppose to compute per-residue RMSDs for the
fit specified by the -fit option (or the default
fitting on all atoms of the molecule if the -fit
option was omitted). <atomlist> should be just the
"atom part" of an NAB atom expression (see below).
It will be used as the atom selection upon which
the RMSD of each residue will be calculated. Nor-
mally, this will be the quoted wildcard character
"*", indicating that all atoms of each residue will
be used to compute the per-residue RMSDs.
ATOM EXPRESSIONS
An atom expression is a pattern that matches one or more
atom names in a molecule or residue. NAB atom expressions
are based on the idea that atoms can be easily specified
by three things: the strand they belong to, the residue
they belong to, and their name. Therefore, an NAB atom
expression consists of three parts: first, a strand part,
second, a residue part and third, an atom part. The parts
must occur in order and be separated by colons (:). For
example, the expression 1:10:CA specifies the alpha carbon
of residue 10 on strand 1.
Not all three parts of an atom expression are required.
If one part is missing, it is assumed that you mean to
select everything for that part. Extending the above
example, the expression 1::CA specifies the alpha carbons
in all residues on the first strand. Notice that there is
nothing for the residue part, so all residues were
selected.
Finally, within each part, the * and ? wildcards and/or
the , and - delimiters and the construct can be used to
increase the flexibility of atom expressions. For exam-
ple, 2:1-10:CA selects the alpha carbons for the first 10
residues of the second strand, while :1-10,ALA:C* selects
all carbon atoms in all ALA residues in all strands as
well as all carbon atoms in the first 10 residues of all
strands.
Some more examples of atom expressions:
::C,CA,N Select all atoms with the names C, CA or N in all
residues in all strands - typically the peptide backbone.
1:1-10,13,URA:C1' Select atoms named C1' (the glycosyl
carbons) in residues 1 to 10 and 13 and any residues named
URA in the first strand.
:C*[^'] Select all non-sugar carbons in a nucleic acid.
The [^'] is an example of a negated character class. It
matches any character in the last position except '.
::P,O?P,C[3-5]?,O[35]? The nucleic acid backbone. The P
selects phosphorous atoms. The O?P matches phosphate oxy-
gens that have various second letters: O1P, O2P or OAP,
OBP. The C[3-5]? matches the backbone carbons C3', C4',
C5', or C3*, C4*, C5* depending on the character you use
to denote "prime" in your structures. The O[35]? matches
the backbone oxygens O3', O5' or O3*, O5*.
NAMING AND NUMBERING CONVENTIONS
This program reads pdb files but doesn't necessarrily keep
the names and numbers for the residues and/or strands that
appeared in the pdb file. Atom names in your pdb file
will be preserved, but by convention, NAB and therefore
suppose start residue numbering over at the beginning of
each strand. Also, strands are labelled as integers
beginning at 1, not alphabetically beginning at A. Be
careful about this since correct atom expressions rely on
the understanding that residues on the second, etc.
strands in particular may be renumbered if they weren't
already in the pdb file.
Example 1:
suppose *.pdb
would take all files with the .pdb extension in the cur-
rent directory, calculate the rms deviation for every pos-
sible pair, calculate the mean structure and report the
overall rms pairwise deviation and the rms deviation from
the mean structure.
Example 2:
suppose -mat -rot *.pdb
Same as example 1, but in addition, the complete matrix of
pairwise deviations as well as each structure's deviation
from the would be printed to STDOUT. The superimposed
structures would be written out as *.rot.pdb
Example 3:
suppose -mat -rot -mean -fit ":1-10:C,CA,N" *.pdb
Similar to example 2, but in addition, the mean structure
would be written to the file "mean.pdb" and the superposi-
tion would be done considering only the backbone atoms of
the first 10 residues of all strands. The deviations
would be calcluated using all atoms.
Example 4:
suppose -mat -rot -mean -fit "::C,CA,N" -calc "::C,CA,N"
*.pdb
Similar to example 3, but both the fitting and the rmsd
calculations would be performed on all of the backbone
atoms in the molecule.
Example 5:
suppose -fit "::C,CA,N" -pr "*" *.pdb
This example shows how to use the per-residue RMSD fea-
ture. The fit expression indicates that the molecules
will be fitted on the backbone atoms, and subsequently,
per-residue RMSDs will be computed using all atoms in each
residue.
Example 6:
suppose -fit "::C,CA,N" -pr "C*,N*,O*,S*" *.pdb
Similar to example 5, except that the per-residue RMSDs
will be computed on the atoms named like "C*,N*,O*,S*".
Namely, all the heavy atoms in each residue.
FILES
Statistics are printed to STDOUT; rotated coordinates (if
requested) are placed in new files that have ".rot.pdb" in
place of the input file extension (usually ".pdb").
DIAGNOSTICS
As soon as the first difference is detected, the program
stops and prints an error message.
If either atom expression fitexpr or calcexpr match no
atoms in the structure the program stops and prints an
error message.
If less than 2 input files are detected the program stops
and prints an error message.
BUGS
Checks are not made that the atoms in are really in the
same order in all structures. This is particularly trou-
blesome for the file specified by the -cmp option since
presumably the comparison pdb file has been obtained from
a different source (i.e. an Xray or Brookhaven structure).
Portions of an atom expression can be invalid and without
warning the program goes ahead and computes the fit and/or
calculation on the valid part of the atom expression.
This can be misleading.
If certain atom expressions are not contained in quotes,
they can be interpreted by the shell and replaced by file-
names, etc. If you are unlucky, undesireable behavior
such as seg faulting and dumping core will result. Put
your atom expressions in quotes.