Cavity.exe within 3V


I am using your program 3V for computing the volume of the active site
of a protein which is clearly external. I am using your program Cavity.exe of
3V. However, I do not know how to interpret the results of the run. It
would be nice if you please help me on this regards,

If the site is external then you are probably looking for a channel
rather than a cavity. Cavities are completely enclosed by the structure.
My suggestion would be to use the AllChannel.exe program and play with
the probe sizes.

The output from can be in several forms, but I typically use the -m
volume.mrc, MRC output and view the results in UCSF Chimera since it is
a free program.

Thanks for your reply. I followed your suggestion and able to visualize the
Channel. But, I am wondering if I could also measure the Channel. Is it
possible by your program?

More specifically, given a structure, can I compute the volume of any
active site using your program? Do you have any other program or webserver
to do that?

I know the latest subversion source code outputs both the volume and
surface area of the channels. The website shows it as well.

It is up to you to get the parameters right, so that you are only
looking at the channel and not the any extra pockets.

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