[Chimera-users] CA-only shown as ribbons
meng at cgl.ucsf.edu
Sun Oct 4 09:46:07 PDT 2009
I believe that it is already ribbon when you open it, but if not, use
"Presets... Interactive 1 (ribbons)" or "Actions... Ribbon... Show."
By ribbon/worms we mean a smooth path through the CA atoms, instead of
the CA trace, which is just a series of bonds between CA atoms and
looks like a zig-zag.
Probably you mean that the ribbon is just a tube of constant width and
does not show secondary structure (where helices and strands are wider
parts of the ribbon, and there is an arrowhead at the end of each
strand). That is because the structures does not have HELIX and SHEET
information at the beginning. You *can* show the ribbon like that,
but you would have to figure out yourself which residues are helix and
strand, and make the assignments yourself. This can be done using the
Selection Inspector, Define Attribute, or the command "setattr," for
setattr r isHelix true :1-10.a,23-36.b
setattr r isSheet true :15-19.a,23-29.a
For details on manual assignment, see methods A, C, D, and E in this
Method B uses the "ksdssp" in Chimera to calculate secondary
structure, but this method cannot be applied to CA-only structures.
I hope this helps,
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
On Oct 4, 2009, at 12:52 AM, Andrei Neamtu wrote:
> Just a quick question:
> I have downloaded the latest daily build of CHIMERA and I want to make
> a ribbon picture only fom the alpha-Carbon trace.
> On the site it is said in the Appearance and Image-Saving section that
> "CA-only and P-only structures can be shown as ribbons and worms "
> I tried but didn't succeded .
> Does anybody know what are the steps in displayng such a structure?
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