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

[James Starlight]

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


2014-03-18 4:08 GMT+04:00 Eric Pettersen <pett at cgl.ucsf.edu>:

> 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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> > Chimera-users at cgl.ucsf.edu
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> >
>
>
>
>
>
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