Computations ar fast, but networking is slow. Our first releases transmit plain atoms coordinates, as long as facet normal vectors coordinates. In later releases we no longer transmit atom coordinates but their index in a list and facet normals are no more transmitted, they are computed by the tcl plugin. In future releases we will also make use of a binary encoding instead of the actual ascii.
No.
Pockets are solely defined on geometric criteria. Furthermore, actually the
alpha shape theory (on which the software is based) does not accomodate very
well with moving spheres.
No
Pockets are solely defined on geometric criteria.
Basically we compute exactly what we promise, nothing more, nothing less.
Now, it is clear that many geometrically defined pockets may not find a true
biological meaning. Any way, we choose to keep the whole bunch of pockets
beacause it is not easy to deiscriminate at first glance. Also, even tiny
pockets can carry information depending on what one is interresterd in. They
can for instance allow for the visualzation of a putative recruitements in
a larger pocket, or give a measure of lacunarity in the protein core.
Nevertheless, there are still meaningless pockets, for instances thoose that
are very thin and mainly composed of mouths. In a future version we consider
to add a functionalitie to let the user filtrate pockets, manually or by the
mean of filters.
It is most probably normal. Check the details about the soft.
