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<h2>Improving Alignments</h2>
The alignments generated by the software can be improved by right
clicking on an embedding in the results tree and selecting <tt>Refine
Alignment</tt>. This will launch the alignment-refinement widget:
<p>
<center><img src="Refine-shot1.jpg"> </center>
<p>
The goal of this widget is to allow you to improve an alignment by
forcing atoms in the embedding closer to atoms in the reference
molecule. This is done by setting up an atom-atom correspondence
between the two molecules (assigning atoms in the aligned structure to
atoms in the reference structure) and then clicking the <tt>Refine
Alignment</tt> button to run the refinement. The updated alignment
will be displayed in PyMol and its important parameters (energy, shape
score, and RMSD) will be displayed in the widget:
<p>
<center><img src="Refine-shot2.jpg"> </center>
<p>When the alignment-refinement widget first opens, a starting
atom-atom correspondence will be automatically generated based on
proximity of atoms in the alignment to those in the reference
molecule. This correspondence is displayed in the correspondence table
using atom indices and in PyMol using distance monitors to connect
corresponding atoms. Clicking on a row in the correpondence table will
cause the selected atom-atom correspondence to be highlighted in PyMol
using atom picks (large spheres). If an atom in the alignment has no
correspondence, selecting its row will highlight only that atom in PyMol.
<p>Clicking the <tt>Clear Correspondences</tt> button will clear all
current atom-atom correspondences and allow you to start afresh.
<p>Some notes about atom-atom correspondences:
<ul>
<li>In general, there does not need to be a correspondence for every atom in
the alignment molecule.
<li>To add new atoms to the atom-atom correspondence, or to alter an
existing correspondence, pick one atom in the alignment and one atom
in the reference molecule, then click the <tt>Connect Picked Atoms</tt>
button.</li>
<li>To clear an existing correspondence, simply click the <tt>Clear
Current</tt> button in that row of the correspondence table.</li>
<li>Left clicking on the column headings in the correspondence table
will sort the table by the contents of that column, clicking again
will reverse the sort order. By sorting on the <tt>Reference Id</tt> column,
you can group together all the alignment atoms that already have a
correspondence established.
</ul>
<p>Once you are satisfied with the refined alignment, clicking the
<tt>OK</tt> button will close this widget and add a new alignment to
the results tree. The new alignment will be selected. Clicking the
<tt>Cancel</tt> button will close the widget and discard the current
refined alignment; the original alignment in the results tree will not
be altered.
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