[Chimera-users] nucleic acid ribbon appearance

Elaine Meng meng at cgl.ucsf.edu
Tue Mar 30 16:06:56 PDT 2010

(previously sent to just Ajith, now sharing with chimera-users)

Hi Ajith,
You can definitely adjust the nucleic acid ribbon size/shape with the  
"Ribbon Style Editor" tool (under Tools... Depiction).

The width/thickness part is easy, you could change numbers in the  
Scaling tab.  The curvature might be harder, since the interpolation  
method is probably different.  Nevertheless, you can change which atom  
positions define the ribbon path in the Residue Class tab.  The Cross  
Section tab lets you draw the shape of a ribbon slice.  In each tab,  
if you have a set of parameters that you like, it can be named and  
saved for later use.

For general information on shininess/smoothness (which also affect  
ribbon appearance), see the tips on image saving:


On Mar 30, 2010, at 2:57 PM, Ajith Harish wrote:

> Hi Elaine,
> I just downloaded the 1.5 daily build. I will use it.
> I will be happy to send you some images that show the difference  
> between RIBBONS and Chimera. I wouldn't know the technical terms  
> associated though and its been a while since I used RIBBONS, its not  
> supported anymore. From what I have seen, it seems like its  
> difference is in the thickness and curvature of the ribbons that are  
> rendered. The difference is seen only with nucleic acids and there  
> does not seem to be any noticable differences for proteins. it I  
> will send some images as soon as I can.
> In case you like to check more on Ribbons, information is here http://www.cbse.uab.edu/ribbons/ 
> .
> Thanks,
> Ajith
> On Mar 30, 2010, at 4:48 PM, Elaine Meng wrote:
>> Hi Ajith,
>> Can you explain a little more about what aspects or features of the  
>> RIBBONS rendering it is that you prefer?  If you have any example  
>> figures or URLs that link to example figures showing what you mean,  
>> that might be helpful too.  We are always interested in hearing  
>> people's opinions, although of course I can't guarantee something  
>> would be changed. Also, if there is some parameter you could change  
>> in Chimera to get an appearance similar to what is it you like,  
>> then I could let you know.
>> Thanks,
>> Elaine
>> P.S. maybe you would be interested in this list of what is new or  
>> different in Chimera 1.5 relative to 1.4/1.4.1:
>> http://www.cgl.ucsf.edu/chimera/docs/relnotes/snapshot.html

>> On Mar 30, 2010, at 2:42 PM, Ajith Harish wrote:
>>> Hi Elaine,
>>> Thank you for the explanation. I currently have version 1.4.1  
>>> build 20308. I got it just a few weeks ago and didn't expect a  
>>> newer version would be available. Great!
>>> Thanks for developing Chimera, its great and easy to use. Although  
>>> this is not the right forum, if you don't mind I would like to  
>>> make a suggestion. For the ribbons representation of nucleic  
>>> acids, I have been using RIBBONS, its rendering is really  
>>> pleasing. Chimera's rendering is close but it would be great if it  
>>> possible to match that of ribbons.
>>> Thanks again.
>>> Best wishes,
>>> Ajith

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