[Chimera-users] Deleting invisible structures?

max taylordavies maxtaylordavies at gmail.com
Wed Aug 31 13:14:10 PDT 2016

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!

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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