I like your paper about 3V tool and I try to apply it on my proteins. However there seems to be a problem with online version – I cannot get to results through the link provided, e.g. http://geometry.molmovdb.org/3v/tempfiles/nchan8269.pdb.gz
I tried both module for cavities and channels with similar failure.
Could you solve it for me please?
I’ve set up a newer server that provides more feedback at http://3vee.molmovdb.org, I keep the old one around since people still prefer it.
All I can tell from looking at the server is that the file you are looking to download does not exist. So, maybe the program crashed. Try the new site and it might be more informative.
I would try Channel Finder instead of Channel Extraction. Channel Extraction is very particular about finding the exact coordinate of the channel — in fact I may change the algorithm to accommodate for this.