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Hi Susanna,
It's best to send questions like this to the chimera-users list rather than me directly so that others can benefit from the answer and since I may not actually be the best person to answer the question. For instance, I have no good ideas about showing cavities effectively with VDW or solvent-accessible surfaces and hope someone else can chime in there.
As for the lack of cavities in your image, did Chimera issue a warning when it computed the surface saying that "[c]alculation of some surface components failed" and that "[a] single component of the surface was calculated"? If so, that means that calculation of interior cavities failed and Chimera is showing the exterior surface only (which the error message does say if you read it in its entirety). That would produce the lack of interior cavities you observed. If you didn't get such a message, can you supply the PDB ID for this structure (or PDB file) so I can investigate? Thanks!
--Eric
Eric Pettersen
UCSF Computer Graphics Lab
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