[Chimera-users] distance dash line thickness in rendering

[Elaine Meng]

Hi Drew,
Thanks for your kind words!  Now I hope you won't change your mind... 

The linewidth as shown in the Chimera window is maintained in a final image, but up to a limit.   That is, graphics drivers can only render the line up to a certain fatness.  When you save a high-res image (more pixels than shown in the Chimera window), especially with supersampling (which makes the initial image NxN times larger than the final image), what you get in the final image  may be proportionally thinner than in the Chimera window.

The image dialog will report (near the bottom) the maximum attainable linewidth in the final image given the requested image dimensions and the supersampling level.

Decreasing the supersampling level and/or image dimensions will increase the attainable line fatness.  Generally supersampling is nice because it smooths edges (pixel stairsteps less visible), so I would first see if 2x2 supersampling ameliorates the problem before turning it off entirely.  I've run into this problem when making images for a paper, and solved it by using the minimum resolution suggested in the author instructions (I forget, 300 or 600 dpi and image no larger than the columns in that journal) with 2x2 supersampling.

For further discussion/explanation, see this previous post:
<http://plato.cgl.ucsf.edu/pipermail/chimera-users/2009-December/004642.html>

A few additional points:
(a) make sure you are using a reasonably new version of Chimera, say 1.6.2, because some older versions didn't fatten the lines to compensate for supersampling

(b) you can make the pseudobonds into sticks instead of lines -- sticks are not subject to this linewidth issue and can be as fat as you like, but not dotted or dashed.  Details in this previous post:
<http://plato.cgl.ucsf.edu/pipermail/chimera-users/2012-August/007863.html>

(c) you could use cylinder or sphere objects to fake a solid dotted or dashed line, but it would be tedious because you would have to figure out the coordinates of each cylinder or sphere yourself (we haven't put anything in Chimera to do it automatically).   See this previous post and command "shape" for creating such objects:
<http://plato.cgl.ucsf.edu/pipermail/chimera-users/2012-August/007868.html>
<http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/shape.html>>

I hope this helps,
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 Oct 7, 2012, at 3:06 PM, Andrew Waight wrote:

> Howdy everyone,
>                I love this program! Anyway I'm trying to make some
> figures with distance dashes included. I can obviously change the line
> thickness (pseudobond display options) in the program, but when I save
> a high resolution image (no pov ray) the line thickness in has no
> effect. What to do? Thanks for your help.
>                                                               Drew Waight
>                                                               Stroud Lab