command: symmetry, option: contact
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
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@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
Thanks, This helps a lot Roberto On Thu, Jul 30, 2020 at 5:45 PM Elaine Meng <meng@cgl.ucsf.edu> wrote:
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@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
Hi Roberto, I added the contact and range options to the ChimeraX sym command. They will be in tonight's ChimeraX builds. Tom
On Jul 30, 2020, at 3:31 AM, Roberto Marabini <roberto.marabini.cnb@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 _______________________________________________ ChimeraX-users mailing list ChimeraX-users@cgl.ucsf.edu Manage subscription: https://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users
Thanks Tom Roberto On Fri, Jul 31, 2020 at 8:15 PM Tom Goddard <goddard@sonic.net> wrote:
Hi Roberto,
I added the contact and range options to the ChimeraX sym command. They will be in tonight's ChimeraX builds.
Tom
On Jul 30, 2020, at 3:31 AM, Roberto Marabini <roberto.marabini.cnb@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 _______________________________________________ ChimeraX-users mailing list ChimeraX-users@cgl.ucsf.edu Manage subscription: https://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users
participants (4)
-
Elaine Meng -
Roberto Marabini -
Roberto Marabini -
Tom Goddard