: C

Jul 1 2004

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

5.3 C

!- cavity is the free space inside a molecule. Here we use a limited definition of a cavity as a fully enclosed space inside a molecule. See the icmCavityFinder macro which identifies and characterizes cavities.
To generate a cavity an skin is generated and converted into grob . We then split this grob into individual connected entities.

!- charge is an electric charge in electron units. You may redefine charges with the set charge command.

!- clipping plane An invisible graphical plane which truncates the view. There two clippings planes: the front one and the back one. The front clipping plane determines the beginning of the visible part of your object, while the back clipping plane is where the visible parts ends. The planes can be moved independently, or in concert (so called "slicing"). In the "FOG" mode the image gradually disappears between the front and the back planes.
!- coil is an irregular conformation ("_" in one-character notation). It is displayed as spaghetti when the ribbon type of representation is used. To assign a residue fragment to coil, do something like this: assign sstructure a_/13:40 "_".

!- column indicates a layout format of several arrays ( iarrays, rarrays, sarrays) with the same number of elements as side-by-side columns. The column format look like this:

 
#>  a   b   c 
   1.  15  "alpha"  
   2.  18  "beta"  
   5.  10  "gamma"

It is also useful to show arrays of a table (see also database).

!- current map usually is the last map loaded by the read map command or created by the make map command. The current map may be changed by the set map command. To find out which one is the current, use list maps.

!- current object usually is the last object loaded by the read object command or created by the build command. The current object may be changed by the set object [ os_object ] command. To find out which is the current one, use list object or show object [ os_object].
You may refer to the current object as a_

!- current table usually is the last table loaded by the read table command or created by the group table command. The current table may be changed by the set table command. To find out which one is the current, use list tables.

!- command an instruction one can execute in the ICM-shell interactively or from an ICM script file. Typically a command consists of a verb (like read or delete ) and a bunch of arguments. The word order in the argument list is not important, if arguments have different types. For example:

 
 display a_//ca,c,n yellow # is as good as ...  
 display yellow a_//ca,c,n # ... inverse

There are exceptions,

if two or more arguments are of the same type, e.g. write "This line" "filename" or superimpose as_select1 as_select2 ,
a complex argument consists of two parts: e.g. delete label i_number or grid["x"] in the plotcommand. In the latter case if the "x" string is not preceded by grid word, it will not be considered.

!- comp_matrix
a residue comparison matrix used by the alignment algorithms. The matrix is loaded automatically together with other library files from the icm.cmp file and can be reloaded later (if you need another matrix) using the read comp_matrix command.
The current matrix can be shown. All elements are properly reordered and multiplied by a factor such that the sum of occurrence-weighted diagonal elements (identities) of the matrix is 1.0 and stored in this form. You can increase all the values in the matrix (a useful operation for low sequence identities) with the set comp_matrix command which has similar effect to reduction of the gapOpen parameter.
The set comp_matrix command also allows to modify weight for specific residue pairs (e.g. set comp_matrix 4. "CC"). Two matrices are recommended: the blosum50 with penalties 2.0/0.15 and the Gonnet matrix (the default) with penalties 2.4/0.15. A number of matrices are provided. You can use your own data file too.
Normalized matrices with diagonal elements equal to 1. Most of the matrices efficient for sequence alignment have different Cii weights. For example, two aligned tryptophanes will get better score than two aligned alanines. The Cij values can also be normalized as follows:

 
Cij_norm = Cij/Sqrt(Cii*Cjj)

This normalization is used in the Score () and Rarray () functions calculating conservation values for each position in an alignment.

!- conf a conformation (actually a set of variables determining the conformation) stored in an ICM stack . You can add a conformation to the conformational stack or load a conformation from the stack.
Example:

 
% icm 
 buildpep "ala his trp"   
 montecarlo 
 show stack 
 iconf>       1       2       3       4       5       6       7 
 ener>    -15.1   -14.6   -14.6   -14.2   -13.9   -11.4    -1.7 
 rmsd>      0.3    39.2    48.0    44.1    27.4    56.6    39.3 
 naft>        1       0       0       1       1       1       0 
 nvis>        4       1       1       4       4       4       1 
 print Nof(conf) 
 7 
 print Iarray(stack)  # returns {4 1 1 4 4 4 1} 
 t = Table(stack)     # more conf parameters 
 for i=1,Nof(conf) 
   load conf i 
   center 
   pause  # hit return 
 endfor

!- cpk abbreviation of "Corey-Pauling-Koltun" who introduced space-filling solid models of atoms. In ICM graphics it means solid representation of van der Waals spheres. Spheres are drawn at van der Waals radii. See also: display

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