Using SequenceCEROSENE is rather straightforward. You can upload a
single structure or an archive containing multiple structures. Here
all common archive formats are supported (.tar, .tar.gz, .zip, .7z,
.rar - provided by
Java Archiving Library
). At the moment, internal processing requires the data to be
specified in Protein Data Bank (PDB) format. In addition, you can
also specify any valid PDB identifier and let the server retrieve
the corresponding structure data in the background. In the advanced
settings section, you may choose which coordinates are to be used in
color embedding. By default, the coordinates of the beta-carbon are
referred to in case of amino acids (alpha-carbon for glycine), but
you may choose between using alpha-carbons, side chain centroids, or
terminal heavy atoms. Note that centroid coordinates are always
considered for ligands, RNA, and DNA!
Further, you can specify if SVG, PNG, PML, CSV are supposed to
be generated in the process. As rendering of an SVG file in the
background can take some time - especially for large structures -
you may consider turning this feature off. For submitting a job, an
ID does not have to be provided necessarily, but you may use this
feature for your own comfort.
Upon submitting a job, you are redirected to the session page, where
a bookmark URL and a list of processed and finished jobs is
presented. You can return to this page via the
tab or the bookmark URL. Your data is exclusively associated to your
session id and is removed from the server after 72 hours. Each job
can be accessed by selecting it from the list and clicking the
button. Again, each job can contain multiple processed structures if
an archive has been provided.
On the result page, generated color encodings are presented.
If multiple structures have been processed in one job, each is
presented in individually selectable tabs. The ProteinViewer (PV, M.
Biasini (2014), "PV - WebGL-based Protein Viewer") and colorized
sequences are fully interactive and interconnected, allowing you to
select residues and regions in the protein in sequence and structure
simultaneously. The Shift key can be used to select multiple
residues and alter PV's behavior. Furthermore, representations can
be downloaded in PNG and SVG format. Raw data is available in CSV
text format. Here, chain id, PDB residue index, one letter code,
reference coordinates, and RGB color contents (ranging from 0-255)
are reported for each residue or compound. The downloadable PML
(PyMOL log file) can be useful to PyMOL users. The corresponding
structure can be loaded into a PyMOL instance and colorized as
proposed by SequenceCEROSENE using the PML script. This allows
working offline with generated color encoded sequences.
If you encounter any bugs or issues with the server, or simply find
this service useful to you, please feel free to
us. Any feedback is very much appreciated :)