[chimera-dev] Feature request

"F.Xavier Gomis-Rüth" xgrcri at ibmb.csic.es
Fri Aug 1 11:31:11 PDT 2014

Wow, thanks a lot to Eric and Elaine for such a useful advice!
Best wishes,

On 1/8/14 8:28 PM, Eric Pettersen 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
>                         Eric Pettersen
>                         UCSF Computer Graphics Lab
> http://www.cgl.ucsf.edu
> On Aug 1, 2014, at 10:13 AM, Elaine Meng <meng at cgl.ucsf.edu 
> <mailto:meng at cgl.ucsf.edu>> wrote:
>> Dear Xavier,
>> Thanks for your kind words!
>> Unfortunately I can’t report any progress in this area.  We did add a 
>> “spring” style, but other than manually calculating coordinates of 
>> small spheres and cylinders and then creating them with command 
>> “shape”, my only other idea for showing dashed lines as 3D objects 
>> via Chimera is to use the “neon” command (not available on Windows). 
>>  It has many options and you can even control the lighting, but it is 
>> noninteractive and the parameters are mainly specified by parameter 
>> files neon.dat and conic.dat.  It can be quite labor-intensive 
>> (iterative) to get what you want.  Also, it does not include text 
>> labels, ribbons, or molecular surfaces: just spheres, ball-and-stick, 
>> sticks, and backbone “tubes.”  I attach an image of the Chimera 
>> window and an image made with the command:
>> neon -o neon.tiff -c conic.dat
>> with parameter files conic.dat and neon.dat both in the current 
>> Chimera working directory.
>> <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/neon.html>
>> <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/neon1.html>
>> Sorry I don’t have a better answer,
>> Elaine
>> -----
>> Elaine C. Meng, Ph.D.
>> UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab
>> Department of Pharmaceutical Chemistry
>> University of California, San Francisco
>> <neon.dat><conic.dat>
>> Chimera window:
>> <chimera.png>
>> neon.tiff using the settings in neon.dat and conic.dat
>> <neon.tiff>
>> On Aug 1, 2014, at 6:51 AM, F.Xavier Gomis-Rüth <xgrcri at ibmb.csic.es 
>> <mailto:xgrcri at ibmb.csic.es>> wrote:
>>> Dear CHIMERA team,
>>> I moved from SETOR to CHIMERA for preparing nice protein structure 
>>> images for publication already some
>>> time ago and am totally happy. Thre is, however, one single feature 
>>> that was possible in SETOR but I still miss
>>> in CHIMERA: to draw pseudobonds as dashed sticks or small spheres. 
>>> Is it be really not possible to implement
>>> this nuisance? I known Elaine negatively answered a similar question 
>>> some time ago within the BB but I would
>>> herewith strike a blow for it again.
>>> Best wishes and thanks for maintaining and devloping such a 
>>> fantastic program,
>>> Xavier
>>> -- 
>>> <fxgr_signanew.jpg>
>> _______________________________________________
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>> Chimera-dev at cgl.ucsf.edu <mailto:Chimera-dev at cgl.ucsf.edu>
>> http://www.rbvi.ucsf.edu/mailman/listinfo/chimera-dev

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