[Chimera-users] Truncate crystals in Chimera

Elaine Meng meng at cgl.ucsf.edu
Wed Mar 18 12:54:37 PDT 2020

Hi Divita,
Chimera is mostly used for biomolecular systems and carbon-containing compounds, so it doesn't have features for working with inorganic nanoparticles specifically.  

However, you can do general things like select atoms with Ctrl-click (and Shift-Ctrl-click to add to the selection) and then use menu: "Actions... Atoms/Bonds... delete"  to delete what was selected. You can also Ctrl-drag a rectangular area to select everything in it, but that's harder to control exactly which atoms you would get.

If you could somehow select only one atom or a few atoms in the middle of the blob, next you could then select all other atoms within or beyond some distance of them (effectively a sphere if you had started with one atom) and then delete them all at once.  E.g. with one atom in the middle already selected, then something like command:

select sel za>15


...would select atoms farther than 15 Angstroms from the currently selected atom, leaving a sphere of atoms with radius 15 unselected.  Then you could use the menu to delete the selected atoms as described above.

Otherwise, you would have to manually trim from the outside by selecting with mouse Ctrl-click as I mentioned first.

I hope this helps,
Elaine C. Meng, Ph.D.                       
UCSF Chimera(X) team
Department of Pharmaceutical Chemistry
University of California, San Francisco

> On Mar 18, 2020, at 7:57 AM, Divita Mathur <dmathur4 at gmu.edu> wrote:
> Hello
> I am a novice in molecular modeling. I have created a gold nanoparticle cube using “make copies” in the Unit Cell option. But it is a cube, and usually gold particles are considered “spherical”. How can I “trim” or truncate a crystal generated via a unit cell? 
> Best,
> Divita Mathur

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