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[ alignment | all | alpha helix | amber | append | atom | axis ]

alignment


[ 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 namedescription
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:

  1. the "Hidden Block Format can use the following special symbols: e.g. " %f .. %t " or " %L "
  2. the "Hidden block width" which defines the total length of the hidden section.


all


an option used in several commands where whole list of items involved should be invoked (e.g. show terms).

alpha helix


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

amber


a force field for simulations of proteins and DNA in the Cartesian coordinate space.
See the reference.

append


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: 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:



atom


(Greek): indivisible; the smallest particle of a chemical element that can exist alone or in combination (cool, isn't it?).

axis


an imaginary straight line passing through a point or a body.

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