One related idea is to use "Actions->Hold Selection Steady" to try to hold the water channel as steady as possible and then select the waters and use "Analysis->Calculate occupancy…" to calculate a volumetric density of the waters inside the channel. The values of the density will vary from 0 to N, where N is the number of frames, so you can vary the volume threshold to see where the high vs. low occupancy areas are. --Eric Eric Pettersen UCSF Computer Graphics Lab http://www.cgl.ucsf.edu On Mar 17, 2014, at 4:33 PM, Elaine Meng wrote:

Hi James, You *could* calculate a molecular surface at each frame (which would have the by-product of calculating SASAs and SESAs), but that is different than actually counting how many waters are in the channel. It depends which of those things you actually want.

The SASA calculation includes per-atom and per-residue values, but unless you have some idea of what to use as a proxy for channel state (e.g. when residue X has SASA > N it means the channel is open), I'm not sure what you would do with them. Once you had decided on some SASA or SESA-related proxy, its value could certainly be reported (e.g. written to Reply Log or file) at each frame.

However, the molecular surface calculation sometimes fails, especially for larger and more complicated structures, so it might not be available for every single frame.

The other approach is to try to actually count the waters in the channel at each frame. It would require figuring out some geometric criterion such as "all waters within N angstroms of atom X" (or some set of atoms or residues). Once you had determined such a specific criterion you could use it as a selector, and then tally up how many water residues are selected at each frame.

Either way, it would require a little Python scripting to report the surface area of interest or to select waters and report how many are selected, with trajectory playback in MD Movie: <http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/movie/framemovie.html> <http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/movie/movie.html#per-frame>

… or in the context of a Chimera command script with playback using the "coordset" command: <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/coordset.html> <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/perframe.html>

Best, Elaine ---------- Elaine C. Meng, Ph.D. UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco

On Mar 17, 2014, at 3:21 AM, James Starlight wrote:

...

Dear Chimera users!

I've performed md simulation of water soluble protein having water-assessable channel in its interior. I'd like to perform analysis of average number of water molecules detected within the protein interior during MD trajectory with the possible visualization of such internal water binding sites. Does SASA calculation which I've seen in vmd could provide me with additional insights? I'd be thankful if you provide me with some Chimera tools suitable for such task.

Many thanks for help, James

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Hi James, After setting up the basic display (i.e. show ribbon, hide atoms/bonds), use the command line to work out the commands that you want to run at each trajectory frame. For example, if your residue of interest is 57 in chain A, maybe something like: ~disp solvent disp solvent & :57.a z<5 Then once you have decided on which commands you want, just use per-frame scripting in the MD Movie dialog, e.g. choose from MD Movie menu: Per-Frame… Define script and enter those commands as a Chimera command script to be run at each movie frame. This is documented here <http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/movie/framemovie.html> <http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/movie/movie.html#per-frame> … and there are further examples in the "Trajectory and Ensemble Analysis" tutorial: <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/tutorials/ensembles2.html> You might also want to take a look at that tutorial to get more familiarity with MD Movie in general. The second part has an example of the occupancy calculations that Eric mentioned. I hope this helps, Elaine ---------- Elaine C. Meng, Ph.D. UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco On Mar 20, 2014, at 3:15 AM, James Starlight <jmsstarlight@gmail.com> wrote:

Hi Elaine, Eric, many thanks for suggestions!

This time I'd like just visualize water influx into the protein interior seen during molecular dynamics trajectory. Previously I did such analysis in VMD but due to some problems with understanding of Chimera's selection lets consider my example more closely here.

E.g I've defined some geometrical center (specifying some residue which is situated within of my protein interior) and than would like to (1) select all water within 5 A of this residue and (2) using MD movie plugin make such selection in each trajectory frame and visualize it along with the cartoon representation of my protein only (hiding all another solvent). I'll be thankful if you provide me with some example of such task. James