-- Java should be enabled in order for the main annotation page to work properly,
i.e. for Java Mage to run.
-- To view kinemages,
Mage should be
downloaded
and you should configure your web browser to handle files of mime-type kinemage with extension kin with Mage.
The command to open the kinemage-file should be
"your_Mage_executable %s" (for Windows %1 instead of %s ;
for Mozilla browsers no parameters needed).
-- To view Rasmol representations,
Rasmol should be downloaded and you should configure your web browser
to handle files of mime type
chemical/rasmolscript
and having extension ras with Rasmol. Note that the command to
open the ras-file should be "your_rasmol_executable -script %s"
(for Windows %1 instead of %s). Be sure that you use Rasmol version
2.6.x or 2.7.2.1, not 2.7.2.
For Mozilla browsers see more detailed instructions.
-- To view Chime/Protein Explorer representations,
download Chime from mdl and install it (only runs on Windows and Macs).
-- To view annotated Webmol representations, be sure that you have
java plugin installed and enabled in your browser. Note that there are
known problems with Webmol visualisation using java 1.4.x for Linux and Irix.
More technical information:
-- Residues in ACTSITE and BINDING records of a SwissProt entry are mapped to the protein structure. Alignment of the sequence derived from the pdb file
to the sequence in the SwissProt entry is used to define SwissProt feature residues
(ACTSITE and BINDING records). Therefore, the SwissProt ID/AC for a homologous protein
can be submitted to define feature residues in the pdb file of interest. Currently,
the feature residues will be transferred from a homologous protein
if a significant sequence alignment around the feature residue is obtained
with the bl2seq program.
-- Prosite patterns with a high probability of occurrence are displayed along with
other Prosite patterns. The relevance of the Prosite patterns to a specific taxonomy class
is not currently checked.
The false positives listed in Prosite are however filtered out using the SwissProt ID/AC.
-- The current version cannot handle the case when multiple residues
have the same residue number correctly.