You can use CAVER but you would have to make all the symmetry mates as one chain in order to fool it. Still better to just do the experiment I think. Either it will work or it won't, regardless of what any software tells you. Just a wild idea : )
On Fri, Jun 27, 2014 at 5:06 PM, Yarrow Madrona <amadr...@uci.edu> wrote: > Hi Reza, > > CAVER is a great tool for this. There is a web version. You can also > download it to customize and run it in the command line. There is also a > Pymol CAVER plug in that works very well. I have even used it to analyze MD > trajectories. You can find it here: http://www.caver.cz/ > > -Yarrow > > > On Fri, Jun 27, 2014 at 4:00 AM, Reza Khayat <rkha...@ccny.cuny.edu> > wrote: > >> Hi, >> >> I'd like to do some soaking experiments with a relatively large molecule. >> Can >> someone suggest a program/method to display the solvent channels of a >> crystal? We have the crystal structure. I'd like to see if the channels >> are large >> enough to allow the molecule to travel to the hypothesized binding site. >> Thanks. >> >> Best wishes, >> Reza >> >> Reza Khayat, PhD >> Assistant Professor >> The City College of New York >> Department of Chemistry, MR-1135 >> 160 Convent Avenue >> New York, NY 10031 >> Tel. (212) 650-6070 >> www.khayatlab.org >> > >
