[Chimera-users] Stick and Ribbon Connection

[Ardian Soca Wibowo]

Hi Elaine,

Thanks for the suggestions. I guess I can clarify the problem. It is simply
a gap between the ribbon and stick at the junction of the two
representations. Please see attached image.

I used the "ribspline card smooth strand" command, and this made the ribbon
coil follow the path of the backbone more closely, however...it changed the
overall representation too drastically from what we are wanting for the
image to be and from other successive images that we have. When having the
ribspline as default and using ribbackbone, main chains of modeled residues
are shown, but sometimes are flying in mid air.

It would be easiest to extend the length of the end of ribbon to go into
the stick representation so that it could be pseudo connected. I guess
there may be no simple correction. If you have anymore suggestions, please
let me know.


Thanks

Soca


On Tue, Jul 17, 2012 at 1:41 PM, Elaine Meng <meng at cgl.ucsf.edu> wrote:

> Hi Ardian,
> I'm not sure if the gap in this situation is due to the ribbon path, or
> simply that the two ends don't quite meet even though their paths are
> coincident.
>
> As for path, the solution is to use a different ribbon spline, such that
> the ribbon more closely matches the true backbone atom positions.   The
> default B-spline path is nice and smooth but can deviate from those
> positions.
>
> Here's a summary and small image:
> <http://www.cgl.ucsf.edu/chimera/features.html#ribspline>
>
> You can control ribbon spline with the command "ribspline" or in the
> molecule model attributes panel.  For example, to use the cardinal spline
> without smoothing (follow exact c-alpha positions):
>
> ribspline card
>
> ... however, then beta-strands look very ripply.  You might want to try
> using the cardinal spline with some compromise smoothing, and see if the
> junction still looks good enough, for example:
>
> ribspline card smooth strand
>
> If it is mainly a gap rather than path mismatch, you can show both ribbon
> and stick for a given residue, and do that for the first and last stick
> residues.  You can enable showing both for a given residue using the
> command "ribbackbone."
>
> 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 Jul 17, 2012, at 8:02 AM, Ardian Soca Wibowo wrote:
>
> > Hello,
> > I have modeled a structure where a portion is model as sticks while an
> adjacent portion is a ribbon. The space between the two representation is
> disconnected. In the overall view of the figure, this broken space is an
> eyesore, thus I would like to know a way/command that will connect the
> disconnected portion between the stick and ribbon representations. Thanks
> in advanced for the help.
> > Ardian
>
>


-- 
Ardian Soca Wibowo, Ph.D.
Postdoctoral Associate
Dann Research Group
Department of Chemistry
Indiana University

Simon Hall Rm. 309
812-856-3216
awibowo at indiana.edu
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