[chimerax-users] command: symmetry, option: contact

[Elaine Meng]

Hi Roberto,
If using that symmetry without the distance filter would give you "extra" copies, maybe it can be done in two steps by first using the symmetry, and then deleting copies that are farther away.  E.g. in ChimeraX something like

sym #1 i,222r copies true
delete #2 & #1 #>3 

The first command uses the symmetry information to make many copies of #1 as #2.1, #2.2, .... and the second one deletes all the #2 submodels that don't have atoms within 3 angstroms of #1.

ChimeraX sym:
<http://rbvi.ucsf.edu/chimerax/docs/user/commands/sym.html>

Specifying distance zones:
<http://rbvi.ucsf.edu/chimerax/docs/user/commands/atomspec.html#zones>

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

> On Jul 30, 2020, at 3:31 AM, Roberto Marabini <roberto.marabini.cnb at gmail.com> wrote:
> 
> Dear all,
> 
>   In chimera I used to use the command
> 
>   sym #0 group i,222r contact 3
> 
> to surround an asymmetric unit cell by its  neighbors.
> 
> I see that, in chimerax,  "sym" no longer has  the option "contact"
> (or the alternative option "range"). Is there any way to get results
> similar to the ones obtained using chiera command
> 
>   sym #0 group i,222r contact 3
> 
> with  chimerax