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Update help page
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skodapetr committed Dec 20, 2021
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Expand Up @@ -17,58 +17,37 @@ <h1 id="user-guide">User guide</h1>
</p>

<h2 id="specify-what-protein-to-analyze">
Specify what protein to analyze
Specify what structure to analyze
</h2>
<p>
There are two options to analyze a protein:
There are three options to obtain a structure:
</p>
<ul>
<li>
PrankWeb can download it automatically from PDB database provided the
protein identification code.
</li>
<li>
A protein PDB file can be uploaded from user's computer. For description
of PDB format, please see its
<a href="http://www.wwpdb.org/documentation/file-format" target="_blank">
official documentation
</a>.
A structure file,
<a href="http://www.wwpdb.org/documentation/file-format" target="_blank">PDB</a>
or mmCif, can be uploaded from user's computer.
</li>
<li>
Provided Uniprot ID PrankWeb can download structure from
<a href="https://alphafold.ebi.ac.uk/">AlphaFold Protein Structure Database</a>.
For this option the structure visualisation is colored using
residue-level confidence scores.
</li>
</ul>

<h3>Homology</h3>
<p>
Besides selecting what protein to analyze, one can also specify whether
evolutionary conservation should be included in the prediction model by
checking the <b>Run conservation analysis</b> checkbox. Note that
calculating conservation score for user-defined protein file can
significantly increase the time of analysis unless you specify its
PDB identification code or upload multiplesequence alignments for homology
calculation.
</p>
<p>
There are three ways how to calculate the conservation score for the
protein:
checking the <b>Use conservation</b> checkbox. Note that
calculating conservation score can significantly increase the time of
analysis.
</p>
<ul>
<li>
You can specify custom alignment file, using which PrankWeb will
calculate the conservation score for your protein.
</li>
<li>
If you know the PDB code of you protein, you can specify in the the
textbox and PrankWeb will calculate the homology from the alignment
in
<a href="http://swift.cmbi.ru.nl/gv/hssp/" target="_blank">
HSSP database
</a>.
</li>
<li>
Fallback method: If any of the previous methods fails or neither pdb
code nor the alignment file is specified, PrankWeb will calculate the
conservation score automatically using alignment of similar proteins.
</li>
</ul>

<h2 id="visualization">Visualization</h2>
<p>
Expand All @@ -91,9 +70,9 @@ <h3 id="structural-visualization-1">Structural visualization</h3>
are displayed with yellow.
</li>
<li>
If conservation is available, the protein atoms is colored with 11
shades of gray according to the conservation score of each residue.
Darker color depicts higher conservation score.
If score, either conservation or residue-level confidence, is
available, the protein atoms are colored with shades of gray according
to the score of each residue. Darker color depicts higher score.
</li>
<li>
To switch between the views of the protein, use
Expand Down Expand Up @@ -159,8 +138,7 @@ <h3 id="sequence-visualization-1">Sequence visualization</h3>
from the structural and sequential point of view. By default, the sequence
view is zoomed out so that the whole protein is displayed. You can use the
trackbar control to zoom in, or select the area with mouse and zoom to the
selection. A snapshot of the sequence can be captured and exported to SVG
(Scalable Vector Graphics) file using the rightmost button.
selection.
</p>

<h2 id="pocket-panel">Pocket panel</h2>
Expand Down

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