[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

                        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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