[Chimera-users] Viewing one biological unit of a model

Elaine Meng meng at cgl.ucsf.edu
Mon Apr 25 15:09:58 PDT 2016

Hi Derrick,
That PDB entry is an “NMR ensemble” including 100 different conformations of the same thing.  You can hide or delete any of those 100.  To first see what you have, show Model Panel from the Favorites menu.  Initially all the conformations are collapsed into a single line with ID “0.1 … 0.100” or something like that.  If you scroll down to click the “group/ungroup” function in the right side of the Model Panel, that entry will expand out (ungroup) to 100 entries.  

You could show any one by clicking to highlight only that line on the left-hand side of the Model Panel, then clicking the “show only” button on the right-hand side, for example.  You can also toggle the Shown checkboxes individually, or highlight multiple lines and “show only” those or “close” (delete) them leaving only the others.

Or you don’t have to use the Model Panel at all.  For example, if the structure was opened as model #0 and  you wanted to hide all except the first conformation, command:

~modeldisplay #0.2-100
 - OR -
~modeldisplay #0.2-end

…or even delete them

close #0.2-end

It might take a few seconds to execute the command.  

Note that a single NMR conformation is not necessarily a biological unit.  It is just one copy of the coordinate set.
I hope this helps,
Elaine C. Meng, Ph.D. 
UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab
Department of Pharmaceutical Chemistry
University of California, San Francisco

> On Apr 24, 2016, at 8:00 AM, Derrick Lau <derrick.lau at student.unsw.edu.au> wrote:
> Dear Chimera,
> Hi. My name is Derrick. I have recently started learning to use Chimera to look at the capsid structure of HIV. I would like some help in the interface. One particular crystal model, the HIV-dimer model PDB 2M8L, strangely loads a bunch of ribbon structures. Would you know the way of switching off other biological unit so I can see one pair of dimer?
> I didn't have this problem with other capsid structures (like 3P05). Your help is appreciated. Thank you in advance.
> Best regards,
> Derrick Lau

More information about the Chimera-users mailing list