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. Regards, Elaine 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@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