[Chimera-users] [chimera-dev] Feature request

Elaine Meng meng at cgl.ucsf.edu
Mon Aug 11 10:02:29 PDT 2014


To clarify this for the chimera-users list, this was a request on chimera-dev for showing dashed and dotted lines as 3D objects (little spheres or cylinders).  Currently Chimera only shows them as flat lines.  My earlier suggestion on the chimera-dev list (link below) was to use neon/conic instead, which offers a lot of control but is noninteractive and not available on Windows.
Elaine

<http://plato.cgl.ucsf.edu/pipermail/chimera-dev/2014/001138.html>


On Aug 11, 2014, at 9:54 AM, Elaine Meng <meng at cgl.ucsf.edu> wrote:

> Dear Xavier,
> I personally don’t recommend the Chimera/Povray approach… my neon/conic suggestion is better-looking, but not as easy as the feature you request.  There is limited programmer time, so I can’t say it will happen, but we can put it on the list of requests.
> 
> You can enable showing backbone atoms at the same time as ribbon with command “ribbackbone” — then try displaying the carbonyls.  You may also need to unchain (avoid drawing long bonds between different carbonyls, e.g. command: setattr m autochain 0). However, the default ribbon path is smoothed, so in some places the backbone atoms will appear to be floating away from the ribbon.  You can try reducing that problem by using a different method to calculate the ribbon path, for example, with command:
> 
> ribspline cardinal smooth strand
> 
> …but see the manual for other command options and parameters.  The cardinal spline tries to follow CA positions, so it is still possible you won’t be able to totally eliminate spaces between ribbon and C atoms.  It may be necessary to show the C atoms as balls (slightly larger than stick-ends) to obscure the gapping.
> 
> The ribbackbone and ribbon path issues are discussed in more detail here:
> <http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/ribbonstyle/ribbonstyle.html#offset>
> 
> I hope this helps,
> Elaine
> 
> On Aug 11, 2014, at 1:48 AM, F.Xavier Gomis-Rüth <xgrcri at ibmb.csic.es> wrote:
> 
>> Dear Elaine & Eric,
>> thanks again for your and Eric's suggestions. The issue is that the POV-Ray rendering is not as attractive as the CHIMERA rendering.
>> Would it be possible to kindly and humbly request that this minor feature be implemented at a certain time point in a new version
>> of the program :-) ?
>> Another issue I have currently problems with:
>> it would be very helpful to be able to display the main-chain carbonyls sticking out from the ribbon at the right place. I tried with the
>> licorize option of the ribbon trace but it was not solving the problem. This is particularly helpful when representing e.g. metal-binding sites.
>> Thanks again for your help and dedication to constantly improve this fantastic program.
>> Best wishes,
>> Xavier
>> 
>> On 1/8/14 9:11 PM, Elaine Meng wrote:
>>> A few caveats of the Povray approach:
>>> In my tests (current daily build), it always makes cylinders with the same aspect ratio regardless of whether I am showing the lines as dotted or dashed in Chimera.  Also, it is hard to tell they are cylinders unless you make the linewidth fairly large.
>>> 
>>> Elaine
>>> 
>>> On Aug 1, 2014, at 11:28 AM, Eric Pettersen 
>>> <pett at cgl.ucsf.edu>
>>> wrote:
>>> 
>>> 
>>>> Hi Xavier,
>>>> 	In addition to Elaine's neon suggestion, if when you save an image you change the rendering from "Chimera" to "POV-Ray" then any dashed or dotted lines will be converted into equivalent cylinders and spheres in the POV-Ray image.  I've attached an image that shows how a distance looks.
>>>> 
>>>> --Eric
>>>> 
>>>> 
>> 
>> -- 
>> <fxgr_signanew.jpg>
> 
> 
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