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

Derrick Lau derrick.lau at student.unsw.edu.au
Thu Apr 28 01:37:47 PDT 2016


Hi Elaine,

Very clear instructions. Thank you very much.

Best regards,

Derrick Lau

PhD student
University of New South Wales - Molecular Machines Group - (02) 9385 8639
*Cellular and Molecular Biology*

2016-04-26 8:09 GMT+10:00 Elaine Meng <meng at cgl.ucsf.edu>:

> 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
> ----------
> 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
>
>
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