[Chimera-users] question about CHIMERA

Elaine Meng meng at cgl.ucsf.edu
Tue Apr 4 09:57:43 PDT 2006

Hi Guy,
> 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 

show sel


~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; ~surf
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):
open myfile.pdb
open myfile.pdb
sel #0:.a
sel invert sel
delete sel
sel #1:.b
sel invert sel
delete 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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