Representation and Animation with Kine Mage

KineMage (kinetic images) is an interactive 3D structure illustration software (Richardson and Richardson, 1992; Richardson and Richardson, 1994) that can be downloaded from ~ rbateman/kinemage/. It is adapted for the structure representation of biochemical molecules by many biochemistry textbooks. The program consists of two components; PREKIN and MAGE. The PREKIN program interprets/converts pdb file (molecule.pdb) to kinemage file (molecule.kin), which is then displayed and manipulated with the MAGE program. Launch the PREKIN program:

• Click Proceed to input the pdb file and to assign the output file (e.g., molecule.kin). This opens the Starting Ranges dialog box, which offers options (radio buttons) for ''Backbone browsing script,'' ''Selection of built-in scripts,'' ''New ranges,'' ''Focus only,'' and Range list and Reset options.

Figure 15.5. Docking by merging files with SPDBV. The docking of trisaccharide (NAM-NAG-NAM) into the active site of lysozyme by merging trisaccharide file (9lyz.pdb) onto lysozyme file (1lyz.pdb). After the merge, only active-site residues (catalytic residues in green and contact residues in blue) and trisaccharide (in red) are selected to display and saved.

Figure 15.5. Docking by merging files with SPDBV. The docking of trisaccharide (NAM-NAG-NAM) into the active site of lysozyme by merging trisaccharide file (9lyz.pdb) onto lysozyme file (1lyz.pdb). After the merge, only active-site residues (catalytic residues in green and contact residues in blue) and trisaccharide (in red) are selected to display and saved.

• Choose Selection of built-in scripts to open the Built-in Scripts dialog box, which offers various scripts for illustrating macromolecules (Figure 15.6). "CaSS" is the default Browsing backbone script connecting all Ca of the backbone plus disulfides, ''mcHb'' gives main chain with hydrogen bonds, "aasc" offers Ca backbone with all the amino acid side chains colored by amino acid types, and "lots" includes mc, sc, ca, and heteroatoms of the bound ligands and water. Two scripts for DNA/RNA are "naba" and ''separate bases.'' The ''ribbon'' representations include (a) a thin ribbon with variable width dependent on the curvature of the backbone (an option for adding an arrow head on ^ strand) and (b) ''ribbon HELIX_SHEET,'' which offers further options for specifying different widths for a helix, ^ strand, and ^ coil and for specifying the number of subunits to be transcribed.

For customerized structural representation (e.g., main chain with side chains of active site residues and bound ligands):

• Select radio button of New Ranges of the Starting Ranges dialog box to open the Range Controls box.

• Enter residue numbers for the start and end residues.

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Figure 15.6. Kinemage built-in scripts page of PREKIN program. Build-in scripts program for converting molecule.pdb file into molecule.kin file according to the selection(s) for structural features to be displayed/manipulated. To terminate the selection, click OK button. For more than one selection (structural features), click "restart this Pass'' button.

• Check mc (main chain), sc (side chain), or ht (heteroatoms of ligands), respectively, and choose either ''OK accept and comes back for more'' for multiple selections or ''OK accept and end ranges'' to terminate the selection.

• Accept defaults from the Focus Options box and specify the subunits to be transcribed in the Run Conditions box.

PREKIN compiles molecule.kin file (ascii text file), which can be read and edited with Microsoft Word or Corel WordPerfect. The kinemage file (*.kin) has the following general organization:

@text: Description of kinemage to enter into the text window. @kinemage i: Starting a new kinemage with numbers (where i = 1,2—n) @caption: List for the caption window @onewidth: All lines 2 pixels wide optional @?viewid {} to @?matrix for displaying different views

@group {identifier} [parameter]: High level display object @subgroup {identifier} [parameter]: Mid level display object @vectorlist {identifier} [parameter]: Low level display object, [color = ] is the most common

{atomid} [-/P/L] x,y,z: Individual vectorlist item e.g. coordinates of atoms derived from *.vw files

The color of structural elements can be changed by changing color description of color = {color} on the appropriate @subgroup or @vectorlist line. The control checkboxes corresponding to @groups are displayed automatically. However, the control checkboxes relating to @subgroup or @vectorlist can be added/deleted by adding/deleting master = {label} on the desired lines where the checkboxes applied. Similarly, the label of the control checkbox can be changed as well. The molecu_i.kin files can be merged in a usual manner. The merged files can remain as independent kinemages (as @kinemage i) or edited to become @group {identifier} within the merged kinemage. The former is displayed under the control of Kinemage menu and is useful if each kinemage consists of different views. The latter offers mechanisms for superimposing structures (if multiple control checkboxes for @group are checked) and animation.

To create animation (displaying structures in successive frames), merge molecu_ i.kin files either by text editor or from the Edit menu of MAGE program. Edit the merged file such that the merged kinemages become @groups. Set parameter of @group to animate (adding an animate statement on @group line, i.e., @group {mergedkinemage} animate). For different views of structures, write molecule.vw (from @viewid to @matrix) from the MAGE program and insert molecule.vw files into the molecu_i.kin file. After editing, save the file as newname.kin or molecule.kin.

The following lysozyme.kin file exemplifies the animated structures of lysozyme and its binary complexes showing different colors for the main chain Ca (white), contact side chains (cyan), hidden (off) catalytic side chains (blue), and bound ligand (orange, NAGs) with multiple control checkboxes (main chain, contact, catalytic and NAGs). @groups are derived from merged molecu_i.kin files which can be animated. @subgroups designate different structural components with different colors assigned by @vectorlists. The statement ''@vectorlist off {catalytic} color = blue master = {catalytic}'' provides a mechanism for highlighting the side chains of two catalytic residues (Glu35 and Asp52) to blue, which is shown initially in cyan via the checkbox.

@kinemage 1 @caption

Lysozyme and its binary complexes. @onewidth @zoom 1.00 @zslab 200 @ matrix

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  • santina greco
    How to label amino acids in kinemage?
    7 days ago

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