[Chimera-users] Stick and Ribbon Connection
meng at cgl.ucsf.edu
Tue Jul 17 14:18:17 PDT 2012
My only other suggestion is to mess around with the ribbon class of the residues at the ends of the ribbons (Tools... Depiction... Ribbon Style Editor, go to "Residue Class" tab). For example if I'm showing up to 137 as ribbon, then 138-140 as sticks, then 141 on up as ribbon, it may be possible to make the gaps a little smaller by selecting the ribbon segment for 137 and setting guide atom to C and Apply (which by default only acts on the selection), then selecting the ribbon segment for 141 and setting guide atom to N and Apply.
However, it may or may not help, depending on the local conformation. The only way to make the ribbon path end exactly at a backbone atom is to use cardinal spline plus ribbackbone so as to show both ribbon and sticks for the C-terminal stick residue (140 in my example). Also I had to set secondary structure of residues 137 and 140 to coil (alias blah :137,140; setattr r isHelix false blah; setattr r isStrand false blah) to make the segue from stick to ribbon look nice.
Sorry I couldn't give a better solution. Maybe others have brilliant ideas?
Unfortunately the spline is for the whole ribbon (you can't use cardinal spline only next to the sticks and B-spline for the rest).
On Jul 17, 2012, at 11:33 AM, Ardian Soca Wibowo wrote:
> 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.
> 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:
> 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 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
> awibowo at indiana.edu
> Chimera-users mailing list
> Chimera-users at cgl.ucsf.edu
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