Copyright © 2020, Molsoft LLC Jun 5 2024
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[ alignment | all | alpha helix | amber | append | array | atom | axis ]
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 Alignment functions and macros:
Examples: read alignment "globins.msf" list alignments glob_fragment = globins[10:36] show glob_fragment delete alignments How to extract a sub-alignment?If you have a large alignment and you want to select a sub-alignment without realigning, use the Align( ali I_indexes ) function. The indexes in term can be returned by the Index( S_name .. ) function if you know the name pattern of interest. Example in which we create an alignment aln and then extract a sub-alignment with a,b,e : make sequence 10 20 # makes rangomd sequences and names them a,b,c,.. align sequence # creates alignment aln # preparations finished show Index( Name(aln) "[abe]" regexp all) # indexes of sequences with names matching the expression aln_abe = Align(aln, Index( Name(aln) "[abe]" regexp all))
GUI allows one to define how a hidden block is displayed. Two parameters can be specified directly from the Tools Panel in the alignment window:
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-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.
Arrays ( array ) may appear in ICM shell as a result of the read xml command. The following functions can be applied to arrays to convert them to a specific type
Index access to specific arrays (e.g. a={1,2,3,4,5,6} ):
(Greek): indivisible; the smallest particle of a chemical element that can exist alone or in combination. ICM functions related to atoms:
an imaginary straight line passing through a point or a body. Here is a recipe on how to create an object with carbons as Z-axis sampling points every Angstrom: n = 30; z_shift = 15. build smiles String("C",n) strip a_ virtual delete a_//h* # mxyz = Matrix(n,3) # x,y,z matrix initiallized for i=1,n mxyz[i,3]=z_shift + i - 1. endfor # set a_// mxyz # assign coordinates
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