[Chimera-users] Detection of Internal water along MD trajectory

Eric Pettersen pett at cgl.ucsf.edu
Mon Mar 17 17:08:40 PDT 2014

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 Pettersen
                        UCSF Computer Graphics Lab

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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