[Chimera-users] question about CHIMERA
meng at cgl.ucsf.edu
Tue Apr 4 09:57:43 PDT 2006
> I am a PhD student in the department of Biochemistry of the Tel-Aviv
> University and often use your great application, CHIMERA.
> Is it possible to view on chimera the selected part only? Regarding
> this, is it possible to split a model to its units (so each
> chain/ligand) will be considered as a model?
Thanks for your kind note!
Yes, you can show just the selected part; for just atoms and bonds, the
~disp; disp sel
would do it. If you also wanted to show ribbon and/or surface for just
the selection, the easiest way would be to undisplay everything and
then display the ribbon and/or surface for just the selected part. In
commands, that would be
ribbon sel; surf sel
You could do the same thing with the menus, but in that case you would
Hide the ribbon and surface before making the selection, then make the
selection, then use the menus to Show ribbon/surface (which would
automatically affect just the selected part).
Currently you cannot split the model into multiple models. However,
there are few ways you could end up with the parts in different models.
(1) edit the file into multiple files before opening in Chimera (this
is only good if you are comfortable with text editing)
(2) select a part you want to make a separate model, write that out
(Actions... Write PDB with "Save selected atoms only" turned on), read
it back in
(3) open the file multiple times and then delete from each model all
the parts you don't want in that model (can be tedious if you have many
chains). For example (commands below; you could also do it with
selecting the part you want and then Select... Invert (selected models)
and then Actions... Atoms/Bonds... delete):
sel invert sel
sel invert sel
This would give model 0 containing only chain A and model 1 containing
only chain B.
I hope one of these options will be useful for you!
Elaine C. Meng, Ph.D. meng at cgl.ucsf.edu
UCSF Computer Graphics Lab and Babbitt Lab
Department of Pharmaceutical Chemistry
University of California, San Francisco
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