[Chimera-users] Deleting invisible structures?

Elaine Meng meng at cgl.ucsf.edu
Wed Aug 31 15:46:52 PDT 2016

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.



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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