[ alignment | all | alpha helix | amber | append | atom | axis ]
[ Alignment gap format ]
or sequence group.
Individual sequences in the group may be just combined and left-justified (no insertions/deletions,
e.g. as an output of group command) or actually aligned (or realigned) with
either pairwise function Align ( seq1, seq2 ) or multiple alignment command
align sequence_group
Pairwise sequence alignment is performed with the
ZEGA (Zero End-Gap Alignment) algorithm.
You can read, write, list, show, delete or edit an alignment.
Flag l_showSstructure allows you to show the secondary structure string which belong to a participating
sequence to be displayed.
When you show the alignment, the consensus string appears
on top. The meaning of consensus characters is explained
below and the string can be extracted with the Consensus( ) function.
A table with relative amino acid numbers for all sequences in the
alignment is returned by the
Table( ali_ ) function.
An array of mean scores for each column of a multiple sequence alignments is returned by
the Rarray( ali [ exact ] ) function.
Coloring 3D models by local alignment strength. Space averaging
See: selectSphereRadius and ribbonColorStyle = "reliability"
Arithmetics:
Deleting some sequences from an alignment To delete a list of sequences from an alignment use the following command:
delete alignmentName only seq1 seq2 ...
To delete sequences selected via the graphics user interface from an alignment use the
delete alignmentName only selection
command.
Example
delete sh3 only Fyn
delete sh3 only selection
Functions:
function name | description
|
---|
Alignpairwise alignment from 2 sequence, or sub-alignment extracted from another alignment, or alignment extracted from tethers in an ICM-molecular object.
|
Consensus( ) | the consensus string
|
Deletion( ) | residue selection of deleted residues
|
Distance( ) | pairwise distance matrix between sequences.
|
Insertion( ) | residue selection of inserted residues
|
Matrix( ali_ ) | distance matrix
|
Name( ) | string array of names of sequences
|
Nof( ) | number of sequences
|
Profile( ) | a profile derived from the alignment
|
Res( ) | residue selection corresponding to the aligned sequence
|
Score( ) | sequence identity, similarity or alignment score for a pairwise alignment
|
String( ) | a multiline string of the alignment (contains '-' and residues)
|
Table( ) | a table with relative sequence numbers (0 for gaps)
|
calcPairSeqIdsFromAli ali l_mode | macro returning pairwise sequence identities from alignment
|
Examples:
read alignment "globins.msf"
list alignments
glob_fragment = globins[10:36]
show glob_fragment
delete alignments
Displaying hidden alignment blocks in GUI. |
GUI allows to define how a hidden block is displayed.
Two parameters can be specified directly from the Tools Panel in
the alignment window:
- the "Hidden Block Format can use the following special symbols:
- %l number of hidden chars
- %L length of the hidden block
- %f hidden from
- %t hidden to
e.g. " %f .. %t "
or " %L "
- the "Hidden block width" which defines the total length of the
hidden section.
an option used in several commands where whole list of items
involved should be invoked
(e.g.
show terms).
alpha-helical conformation. Average angles (phi=-63.2,psi=-38.5).
Referred to as 'a' in
variable restraint
names: e.g. alpha-zone for histidine is called "ha".
See also commands
assign sstructure
,
set vrestraint
and file
icm.rst
a force field for simulations of proteins and DNA in the Cartesian coordinate space.
See the reference.
used as option mostly in read and write commands, for example:
write matrix "fil.mat" append
read stack "mc12" append
arrays. ICM-shell allows 4 types of arrays:
- iarray - integer array,
- rarray - real array,
- sarray - string array
- parray - pointer array of binary objects (e.g. chemicals, slides, etc.)
These arrays are legal elements of the ICM-shell.
iarray-constant looks like this: {2, 4, 67, -4}.
rarray-constant looks like this: {2.0, -4., .67, -4.3433}.
sarray-constant looks like this: {"a-word","b-word","c-word","..."} .
parray-constants do not exist, a parray can be created in ICM or read from a file.
Commas are optional unless you have negative elements in integer or real arrays.
Array ICM-shell variables can be created by direct assignment:
(e.g.
a={2, 4, 67, -4} or
b={"wow","oops","ouch"} ), read (e.g.
read iarray "numb.iar" ), and written to a file (e.g.
write numb "numb" ).
You can specify a subset
of an integer array (e.g. a[2:15]). Besides, there all kinds of
operations and
functions
on the ICM arrays. There are many ways to create an array:
- read an array from a file: read rarray "a.dat"
- create by direct assignment: a={1, -2, 3, 14}
- use arithmetic expressions: a=Sin(Cos(a))*b
- use functions
Iarray,
Rarray, or
Sarray, e.g.: a=Rarray(15, 2.)
- concatenate two elements, e.g.: a=2//3
(Greek): indivisible; the smallest particle of a chemical element that can
exist alone or in combination (cool, isn't it?).
an imaginary straight line passing through a point or a body.