| Features
of BioEditor
BioEditor
is a standalone Windows program that can be used with Windows
NT, Windows ME and Windows 2000 operating systems. BioEditor
contains features that enable the user to enter text, graphics,
sequence, dynamic structural images and references. Many
features link directly to resources on the World Wide Web.
It
is designed to be used by structural scientists reporting
and evaluating their data, as well as by educators and students
who are seeking to relate structure to function in biological
macromolecules. The interface consists of a series of drop-down
menus and toolbars and three working areas: folders, comments
and palette. The current version of BioEditor contains six
types of entries:
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AUTHOR
To add an author to the annotation, simply click on the
authors icon and a screen appears, with blanks for
pertinent information. When the checkbox for list all
Medline articles published by the above author, a browser
window automatically appears in BioEditor which contains
a Pubmed search for the author by name.
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TOPICS
This is the text area. Documents created in this area are
actually produced in an XML format. Once an annotation is
complete, the document can be published for viewing on Netscape.
It is also possible to embed graphics, sequence (FASTA format),
and dynamic structural images directly in a Topic page.
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STRUCTURES
Structure files in a PDB format can be uploaded to BioEditor
and used to prepare molecular views. It is also possible
to modify the structure files directly within BioEditor
and use the modified files to prepare molecular views.
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PREPARING
MOLECULAR VIEWS
Once the structural files have been uploaded into BioEditor,
they can be used to prepare 3D molecular views in a Chime
window. The window also includes an optional "view
editor" insert that can be used to prepare an animated
sequence of images. The window has all the capacity of Chime
(using the right mouse click to select atoms or residues,
for example) as well as the command line interface that
is associated with Rasmol.
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GRAPHICS
BioEditor can import graphics in *.gif, *.jpg and *.bmp
formats. They can be stored under Graphics in the Folder
window, or inserted directly into a document.
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REFERENCES
The reference tool is currently set up to accept a PubMed
ID number.
When
you click on the PMID in the References folder, BioEditor brings up the full PubMed
reference in a functional browser window. You can use the reference information,
or do further PubMed searches without leaving BioEditor. 
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