I know you have asked for frames, but I assume that each frame is mapped to a
state. The selection logic allows for you to specify the state.
So if the waters of interest are in state 1,40:
python
for i in range(1,41):
cmd.select("wat_"+i,"byres in <mdobjetct> within 6 of
<residue_of_interest>",state=i)
python end
J
> 'sele wats, byres res
> WAT in <md_obj> within 6 of
> <residue of interest>',
On Jul 1, 2013, at 12:42 PM, Matthew Baumgartner <[email protected]> wrote:
> Hi,
> Is it possible to force a selection to only apply to the specific frame
> rather then across frames?
> I'm running in to a problem where I have some (~40) frames from an
> explicit solvent MD that I want to look at. What I want to do is look at
> water molecules around a specific residue at each frame, but when I do
> something like, 'sele wats, byres resn WAT in <md_obj> within 6 of
> <residue of interest>', it ends up a majority of the waters in the
> system. I think that what it is doing is finding all waters that are
> with 6 A of the residue of interest in ALL frames, then selecting them
> in the current frame. Which is not the expected behavior.
>
> From what I can tell, there isn't a selection syntax for selecting the
> frame. Perhaps there is a setting for this that I couldn't find.
>
> Any help would be appreciated including solutions involving VMD or
> custom scripts.
>
> Thanks,
> Matt
>
> --
>
>
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