The annotation format is fully XML-compatible. DTD can be found here.

All annotations should be within <protein name=the_name_of_the_protein> and </protein> tags.
Each annotation should be within <item> and </item> tags.
The following descriptors are supported for annotations (items):

• <group><super>Super-group name</super>_{Sub-group name}</group> .  These define the way of grouping the annotations by the annotation selector.  Namely, each Super-group will appear as a separate table with columns containing Sub-groups.  Annotation selector is able to show one or more selected (all if none selected) Sub-groups of annotations.   Additionally, the selected annotation are sorted and grouped according to Sub-groups in WebMol visualisation.  The names of groups can be arbitrary, the examples are:
• Super-group: Organism; Sub groups: Human, Mouse, etc.
• Super-group: Impact; Sub groups: Activity, Expression, Lability, etc.
• Super-group: Location; Sub groups: Active Site, N-terminal, Surface, etc.
• Super-group: Source; Sub groups: BRENDA, PMD, SwissProt, OMIM, etc.
• Super-group: ProSAT1; Sub groups: SP Active Site, Prosite F1 Site, Prosite F2 pattern, etc.

• <color>color_name</color> The name of the color for the initial appearance of the annotation. (check supported color names here).  The colors then can be changed interactively.  If no color indicated then the default color will be used (black).
• <state> on or off </state> Highlighting of the annotation on or off in the initial appearance of the annotation (default is off).
• <range pdb="1234">123:A 123:A, 456:B 789:B</range> One or many residue ranges separated by commas; each residue range is the numbers of first and last residue with chain ID, like 123:A - residue number 123 of chain A of the pdb file 1234.pdb.  Annotation of several pdb files simultaneously is supported, and indication of pdb id means that the residue ranges are for indicated pdb file.  If the pdb file does not have any chain identifiers, _ (underscore) should be used as id in the residue range definition.
  
• <shortname>name</shortname>The text to appear on the annotation highlighting button.  Supposed to be short, because the text on the button will appear in one line.
• <context>description</context>Longer description of annotation, can be viewed selecting "Details" after right-mouse_click (in some systems thr middle-mouse-button) on the annotation button.
• <link>weblink</link>Http link to the web page, where some description of the annotation can be found (designed to support PubMed abstract).  Acceesible by selecting "Details" after right-mouse_click on the annotation button - the link is printed and can be opened pressing the button "Open new browser window".
  

<?xml version="1.0" encoding="utf-8" ?>
<protein name="haloalkane dehalogenase">
<item>
<color>yellow</color> <group>
		<super> organism </super>
		<sub> Xanthobacter autotrophicus </sub>
	</group>
	<group>
		<super> impact </super>
		<sub> kinetics </sub>
	</group>
	<group>
		<super> source </super>
		<sub> brenda </sub>
	</group>
	<range pdb="pdba">172:A 172:A</range>
	<shortname> F172W </shortname>
	<link> http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&amp;cmd=Search&amp;doptcmdl=DocSum&amp;term=9261999 </link>
	<context> mutant with 10fold higher KM for 1-chlorohexane and 2fold higher KM for 1,2-dibromoethane, increased bromide release but velocity of hydrolysis of alkyl-enzyme bond remains unchanged</context>
</item>
<item>
<color>yellow</color>
	<group>
		<super> organism </super>
		<sub> Xanthobacter autotrophicus </sub>
	</group>
	<group>
		<super> impact </super>
		<sub> mechanism </sub>
	</group>
	<group>
		<super> source </super>
		<sub> brenda </sub>
	</group>
	<range pdb="pdba">172:A 172:A</range>
	<shortname> F172W(1) </shortname>
	<link> http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&amp;cmd=Search&amp;doptcmdl=DocSum&amp;term=11467952 </link>
	<context> steady state kinetics of the mutant compared to the wild-type enzyme</context>
</item>
<item>
<color>yellow</color>
	<group>
		<super> organism </super>
		<sub> Xanthobacter autotrophicus </sub>
	</group>
	<group>
		<super> impact </super>
		<sub> kinetics </sub>
	</group>
	<group>
		<super> source </super>
		<sub> brenda </sub>
	</group>
	<range pdb="pdba">172:A 172:A</range>
	<shortname> F172Y </shortname>
	<link> http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&amp;cmd=Search&amp;doptcmdl=DocSum&amp;term=9261999 </link>
	<context> mutant with 5fold higher KM for 1-chlorohexane</context>
</item>
<item>
<color>yellow</color>
	<group>
		<super> organism </super>
		<sub> Xanthobacter autotrophicus </sub>
	</group>
	<group>
		<super> impact </super>
		<sub> binding </sub>
		<sub> mechanism </sub>
	</group>
	<group>
		<super> source </super>
		<sub> brenda </sub>
	</group>
	<range pdb="pdba">294:A 294:A</range>
	<shortname> F294A </shortname>
	<link> http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&amp;cmd=Search&amp;doptcmdl=DocSum&amp;term=10508409 </link>
	<context> mutant with modified kinetic mechanism for halide binding</context>
</item>
<item>
<color>blue</color>
	<group>
		<super> organism </super>
		<sub> Xanthobacter autotrophicus </sub>
	</group>
	<group>
		<super> impact </super>
		<sub> activity </sub>
	</group>
	<group>
		<super> source </super>
		<sub> brenda </sub>
	</group>
	<range pdb="pdba">289:A 289:A</range>
	<shortname> H289Q </shortname>
	<link> http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&amp;cmd=Search&amp;doptcmdl=DocSum&amp;term=7737973 </link>
	<context> GJ10, mutant with 660fold reduced activity with substrate 1,2-dibromoethane</context>
</item>
<item>
<color>yellow</color>
	<group>
		<super> organism </super>
		<sub> Xanthobacter autotrophicus </sub>
		</group>
	<group>
		<super> impact </super>
		<sub> binding </sub>
		<sub> mechanism </sub>
	</group>
	<group>
		<super> source </super>
		<sub> brenda </sub>
	</group>
	<range pdb="pdba">197:A 197:A</range>
	<shortname> T197A </shortname>
	<link> http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&amp;cmd=Search&amp;doptcmdl=DocSum&amp;term=10508409 </link>
	<context> mutant with modified kinetic mechanism for halide binding</context>
</item>
<item>
<color>yellow</color>
	<group>
		<super> organism </super>
		<sub> Xanthobacter autotrophicus </sub>
	</group>
	<group>
		<super> impact </super>
		<sub> notclassified </sub>
	</group>
	<group>
		<super> source </super>
		<sub> brenda </sub>
	</group>
	<range pdb="pdba">175:A 175:A</range>
	<shortname> W175F </shortname>
	<link> http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&amp;cmd=Search&amp;doptcmdl=DocSum&amp;term=10231528 </link>
	<context> mutant with no inhibition through halide product</context>
</item>
<item>
<color>yellow</color>
	<group>
		<super> organism </super>
		<sub> Xanthobacter autotrophicus </sub>
	</group>
	<group>
		<super> impact </super>
		<sub> notclassified </sub>
	</group>
	<group>
		<super> source </super>
		<sub> brenda </sub>
	</group>
	<range pdb="pdba">175:A 175:A</range>
	<shortname> W175Y </shortname>
	<link> http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&amp;cmd=Search&amp;doptcmdl=DocSum&amp;term=10231528 </link>
	<context> mutant with no inhibition through halide product</context>
</item>
<item>
<color>blue</color>
	<group>
		<super> source </super>
		<sub> SwissProt </sub>
	</group>
	<range pdb="pdba"> 124:A 124:A,260:A 260:A,289:A 289:A</range>
	<shortname> SP_ActSite </shortname>
	<context> SwissProt Active Site </context>
</item>
<item>
<color>bluetint</color>
	<group>
		<super> source </super>
		<sub> SwissProt </sub>
	</group>
	<range pdb="pdba"> 125:A 125:A,175:A 175:A</range>
	<shortname> SP_Binding </shortname>
	<context> SwissProt Binding </context>
</item>
</protein>