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luponzo86 committed Jun 20, 2020
2 parents f21f71c + feb60bc commit 9840bba
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7 changes: 4 additions & 3 deletions faqs.php
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<li id="FAQ-environment">
<h5>What does it mean to include "environmental effects"?</h5>
<p><small>When computing structural and dynamical features from a PDB
structure, by default Rhapsody will only consider a single chain and ignore
structure, by default Rhapsody will only consider a single chain (the one with
higher sequence similarity with the given Uniprot sequence) and ignore
other chains that might be present in the PDB file. Sometimes, for instance
in the case of multimers or other complexes, the presence of other chains
should not be ignored and those properties should be computed for the entire
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ROMK tutorial</a>). In conclusion, environmental effects should be
included if the chain of interest is part of a "stable" complex (e.g. a
multimer) and as such its dynamical properties are influenced and determined
by the presence of other chains. On the other hand, computing predictions on
large complexes will take a significantly longer time.
by the presence of other chains. On the other hand, please be aware that
computing predictions on large complexes will take a significantly longer time.
</small></p>
</li>
<li id="FAQ-legend">
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