[ defCell | accFunction | gapFunction | I_out | M_out | R_out | R_2out | S_out | swissFields | readMolNames | Selection variable | as_out | as2_out | vs_out ]
the
real array
of the default cell parameters. This definition is used in the
Resolution
and
MaxHKL
functions if cell parameters are not provided as arguments.
Default: {1. 1. 1. 90. 90. 90.}
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the real array of the solvent accessibility penalty parameters (as described in
Batalov and Abagyan, 1999).
It contains the values of a, b, c and E damping parameters
for amino acid substitution scores. Generally, if a residue is completely
buried ( Area=0), its substitution scores will be used without changes. If it is
completely exposed, its substitution scores will be multiplied by the
minimal possible value of a. Between these cases the substitution scores
are modulated by a smooth ("arctangent") function with a saddle point at Area=c,
where the slope will be -b. The fourth parameter is reserved for development.
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This definition is effectively implemented in the Align( seq_1 seq_2 area ) },
Score functions and find database command.
Default: {0.33 2.35 0.211, -15.0}.
See also: alignMethod .
the real array of the gap penalty parameters,
which represent a piecewise-linear concave function (as described in
Batalov and Abagyan, 1999).
ATTENTION: at the present time this gapFunction is only active when
alignMethod =2.
The first two values replace
gapOpen and
gapExtension traditional values.
If present, the third element of the array represents the length of the gap,
starting at which further gapExtensions become equal to the
fourth element of the array. Likewise, if more elements are present, they
represent pairs of the threshold lengths of the gap and the new gapExtensions
values. For example,
gapFunction = {2.4 0.15 10. 0.05 20. 0.}
means that
- gap penalty=2.25+0.15*L for L={ 0..10} (and for L=1 it is 2.4= gapOpen ),
- gap penalty=3.25+0.05*L for L={11..20} and
- gap penalty=4.25 for L>20
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The calculations are fastest for the traditional two-element gapFunction.
The three- or four-element gapFunction invokes the optimized routines and
is 50-70% slower. The general kind gapFunction costs approximately 70-90%
additional time for every pair of gapFunction values.
If the last gapExtension is zero, it may be omitted.
This definition is effectively implemented in the
Align , Score functions and
find database search command.
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Default: {2.4 0.15}.
Recommended (put it in your
_startup file): gapFunction = {2.4 0.15 10.}
This set will produce fast and structure-like alignments.
See also
alignMethod, and accFunction (the accessibility attenuation parameters).
an
integer array
in which the output of some commands is stored.
matrix
in which the output of some commands is stored.
real array
in which the output of some commands is stored.
Functions returning in R_out:
- Axis # middle point of the axis
- Disgeo # returns error sum of negative scaled eigen values in R[0], and first three 3 scaled eigen values
- LinearFit # residuals
- Xyz(
.. ) returns inverse transformation
- learn returns model accuracy and stds.
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auxiliary rarray. Used in addition to R_out.
string array
in which the output of some commands is stored.
string array
of SWISS-PROT fields to be read by default in
read sequence swiss
If the field name starts from a minus ('-'), this field will be ignored in
the feature table list.
Example:
swissFields={"-HELIX ","-COIL ","-STRAND","-TURN "}
# to suppress the FT records with the secondary structure info
string array
in which the SDF-file comment fields containing database compound identifier and
description are preset.
There is a standard place where database compound identifier should be stored in SDF (MOL)-files.
This is the first line of the entry.
However most of the database providers got used to leaving this line empty.
Instead they put identifier and description in the end of the file in the following fashion:
...
M END
> <CAT_NO>
R150002
> <NAME>
(5-OXO-HEXAHYDRO-PYRANO[3,2-B]PYRROL-1-YL)-ACETIC ACID METHYL ESTER
$$$$
In this particular case before using such database set
readMolNames = {"<CAT_NO>" "<NAME>"} # useful for Sigma-Aldrich files
Another example:
readMolNames = {"<CODE>" "<IUPAC_NAME>"} # useful for ACD database
Named Atom/Residue/Molecule/Object/Variable Selections |
Selections of atoms, residues, molecules, objects or
internal variables (torsions, planar angles, bond lengths) can
be stored in variables.
Examples:
cc = a_//ca # created named selection variable cc
show cc & a_/3:15 # use it in the expression
In this case the named selection cc is a true ICM-shell variable,
not just an alias for the Ca selection. Please do not confuse it with
another useful mechanism which allows you to use a string
in a selection. This mechanism is used in scripts and macros.
Example:
cc = "a_//ca" # in this case cc is a string, not a selection
show $cc & a_/3:15 # $cc is replaced by a_//ca before parsing
How to store and exchange selections in strings:Examples of using the String ( os|ms|rs [name|number] ) function to return a residue selection:
l_showResCodeInSelection = yes # the default
res_str = String( Res(Sphere( a_H [1] a_A//!h*,ca,c,n,o 3.5 ))) # same as with option String(.. name)
show res_str
a_2c0cb.b/^T159,^S205,^K209,^Y224,^V248,^Y275,^L305,^M356,^N361
# or
l_showResCodeInSelection = no
res_str = String( Res(Sphere( a_H [1] a_A//!h*,ca,c,n,o 3.5 ))) # same as with option String(.. number)
show res_str
a_2c0cb.b/159,205,209,224,248,275,305,356,361
However, be careful with using it in an arbitrary case at the atomic level since it may lead to a string that is too long.
an atom/residue/molecule/object selection variable where
some commands or functions store their output:
If atoms a_1./3/ca,c,n relate to atoms a_2./45/ca,c,n, then the first
set will end up in as_out and the second in as2_out.
the second set of atoms ( selection ) returned by the following commands and functions:
See also: as_out.
The variable selection where some commands or functions store their output: