: A

Jul 1 2004

Contents


Introduction
Reference Guide
User's guide
References
Glossary
A
B
C
D
E-H
S
T
U-Z

Index

5.1 A

!- add a family of commands adding things. It is also used as an option equivalent to append in write command.
!- alignment
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:

extracting a domain (i.e. a certain position range) from an alignment alignment[i1:i2] or alignment[i]
extracting an alignment of a group of sequences from a larget alignment Align(aliLarge, I_seqNumbers )
projected alignment: concatenation of two alignments sharing the same sequence. The shared sequence serves as a ruler for merging the two alignments. The alignments can be of arbitrary size and number of sequences. In the simplest case of three sequences a, b, c and alignments ab and bc, the operation ab//bc will create an alignment of three sequences a b c. The function Align(ab//bc,{1,3}) will extract the, so called, projected alignment of a and c through b. Example:
```
 
  ali1    //    ali2  returns   Projected ali. 
a VYRWA-W     b FK-WG--KW     a  VYR-WA---W 
b -FKWGKW     c AKGWAPGKW     b  -FK-WG--KW 
                              c  -AKGWAPGKW 
```
projecting a numerical property from a sequence to alignment: Rarray( R_property,seq_,ali_,r_gapDefault ).
projecting a numerical property from alignment to a sequence : Rarray( ~R_ali,ali_from,seq_|i_seqNumber )

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 subalignment 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`( )	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)

Examples:

 
 read alignment "globins.msf" 
 list alignments 
 glob_fragment = globins[10:36] 
 show glob_fragment 
 delete alignments

!- 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 3 types of arrays:

iarray - integer array,
rarray - real array,
sarray - string array

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","..."} .
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

!- 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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