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Thanks a lot to everyone who give suggestions on cavity calculation, they were really helpful. Here is a summary of responses:
For cavities the gerargd kleywegts VOIDOO is suitable. It is
available from the O homepage I believe.
Jean Paul Renaud:
Try VOIDOO (GJ Kleywegt & TA Jones, Acta Cryst., D50, 178-185 (1994)) at:
This program detects cavities and calculates their volume in three ways:
the Van der Waals volume (the complement of the molecular Vanderwaals
surface), the probe-accessible volume (the cavity volume that can be
occupied by the centres of probe atoms), and the probe-occupied volume (the
volume that can be occupied by probe atoms).
Also check out the CAST server at: