[Chimera-users] Deleting invisible structures?

[max taylordavies]

Hi Elaine,

Okay, no worries regarding the lack of command-line compatibility, manual
use will be fine!
Thanks again for your help!

Best,
Max

On Wed, Aug 31, 2016 at 11:46 PM, Elaine Meng <meng at cgl.ucsf.edu> wrote:

> Hi Max,
> You’re welcome, of course!
>
> Sorry, I can’t think of any command-line way to select all the atoms that
> aren’t hidden by the per-model clipping plane.
>
> Scene export has further limitations, such as OBJ always including the
> whole surface even if partly undisplayed.  I see that our docs say X3D does
> support per-model clipping planes, but then the issue is whether the
> program you are using to display or otherwise process the resulting X3D
> file interprets that information correctly.
>
> <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/export.html>
>
> Best,
> Elaine
>
> On Aug 31, 2016, at 1:14 PM, max taylordavies <maxtaylordavies at gmail.com>
> wrote:
>
> > Hello Elaine,
> > Thanks for the response! Okay, I didn't know about the distinction
> between undisplayed atoms and those hidden by clipping; I was just talking
> about the latter. I was intending to export the scene in x3d or OBJ format
> rather than write a PDB, but your second trick is very useful! Just to
> check, there's no way to implement it from the command line? It isn't
> super-important if not, just wondering.
> >
> > Thanks again!
> > Max
> >
> > On Wed, Aug 31, 2016 at 8:57 PM, Elaine Meng <meng at cgl.ucsf.edu> wrote:
> > Hello Max,
> > There is a distinction between undisplayed and hidden by clipping, and
> also it matters whether you are trying to save atomic coordinates or
> something else, and in what format.
> >
> > I can speak to the saving of atomic coordinates in PDB format, and in
> that case:
> >
> > (1) if atoms are actually undisplayed (as opposed to suppressed by
> ribbon or hidden by clipping), you can specify them on the command line,
> for example to delete them: delete ~ @/display
> > There is also an option in File… Save PDB to “save displayed atoms only”
> and a corresponding option to the “write” command.
> >
> > (2) here’s a trick for specifying only the atoms that are not hidden by
> clipping, but it requires interactive use: with the clipping in effect, use
> Ctrl-drag to “box-select” everything that is visible.  Then if you turn off
> clipping it will still only have the previously unclipped stuff selected.
> Be aware that selecting a ribbon segment in this way selects all atoms in
> the corresponding residue(s), even if they were or would be hidden by the
> clipping plane.  You can  use “sel” in the command line to specify the
> selection, or “~sel” to specify what is not selected (or invert
> selection).  For example, if you’d selected all the unclipped parts, you
> could delete the remaining atoms with command: delete ~sel
> >
> > The above are atomspecs in that they work in the command line.  I’m
> guessing  by  “the usual atom-spec approach” you meant using residue
> numbers and atom names.
> > 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 Aug 31, 2016, at 9:50 AM, max taylordavies <maxtaylordavies at gmail.com>
> wrote:
> >
> > > Hello all,
> > >
> > > Is there any way to selectively delete the 'invisible' (undisplayed)
> parts of a structure and keep the visible parts without having to use the
> usual atom-spec approach? For example, if I run per-model clipping on a
> protein, is there any way to delete the part that has been rendered
> invisible by the clipping? If this isn't possible, is there a way to export
> only the visible/displayed components of a scene?
> > >
> > > Many thanks in advance,
> > > Max Taylor-Davies
> >
> >
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