[Chimera-users] 3D dashed lines

Elaine Meng meng at cgl.ucsf.edu
Sun Nov 28 09:35:52 PST 2010

Hi Sundar,
In the "structure analysis and comparison" tutorial images, the  
pseudobonds are flat lines, but I can see why you might think they  
were 3D dots or dashes: the dashed line is fairly thick, and sometimes  
the atoms on the ends are small balls.

On Nov 27, 2010, at 6:55 PM, M Sundaramoorthy wrote:

> Hi Elaine,
> Thanks for your prompt reply. Perhaps, I imagined dotted stick in  
> the image of 2zcp active site in Analysis/Comparison tutorial. I'll  
> just stick to what is available now.
> On the Side View panel, I found extremely faint grey square/lines  
> and now my eyes are trained to find them.
> Regards,
> Sundar
> On Sat, Nov 27, 2010 at 3:47 PM, Elaine Meng <meng at cgl.ucsf.edu>  
> wrote:
> Hi Sundar,
> Currently there is no dashed or dotted stick option for pseudobonds  
> in the interactive view, sorry.  I don't know which tutorial image  
> you mean -- I made the tutorials in the User's Guide and I'm pretty  
> sure they don't have any such images.
> I can think of one way to make dotted or dashed stick pseudobonds in  
> a static image from Chimera, but that is with the "neon" command,  
> which is not available on Windows.
> <http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/neon.html>
> Raytracing with Povray from Chimera will make a static image with  
> solid stick pseudobond even when it is shown as a line in the  
> interactive view, but even if the line is dashed or dotted, the  
> stick is continuous (unfortunately).  At least, that's what happened  
> just now when I tried it in recent builds of both version 1.5 and 1.6.
> <http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/raytracing.html>
> I can't answer the Side View part, but it might be a graphics driver  
> issue -- you could try updating your graphics driver.
> Regards,
> 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 Nov 27, 2010, at 8:59 AM, M Sundaramoorthy wrote:
> > I like to show pseudobonds (H-bonds, metal coordinations and  
> distances) as solid dotted or dashed lines.
> >
> > To draw dashed/dotted line I can choose dashed line style in the  
> Pseduobond attributes panel. But it works only with bond style  
> 'wire' not with 'stick'. It can essentially draws flat lines. How do  
> I show 3D dashed/dotted lines? Some images in the tutorial do have  
> such lines represented as dotted (spheres) lines.
> >
> > Another problem I have is that the Side View panel shows the image  
> but does not show the eye (the small square) and the clipping planes  
> (vertical lines). I am using Chimera 1.5rc in Windows Vista.
> >
> > Thanks
> > Sundar

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