[Chimera-users] Question: how can I render pseudobonds visibly when saving as Chimera-highres-image]

Dietlind Gerloff dgerloff at ffame.org
Fri Aug 29 15:21:27 PDT 2014

Dear Elaine and Tom and other Chimera-developers/maintainers,

I cannot tell you how much I admire (and appreciate) what you
have done with Chimera !!! I am just getting the last touches
on a collaborative paper with colleagues from the University
of Edinburgh and I used Chimera for much of the modelling
of a large protein (Condensin) and for lovely images as well.
We'll make sure we give you proper credit!

One thing I'm having problems with - I am now trying to
save image in high-resolution (600dpi) that show pseudo bonds
Each pseudobond highlights a distance constraint, i.e. they
are drawn by the distance function/monitor and are visible
beautifully on the screen.
However, when I save (as .png, .jpg or whatnot) the pseudo bond
doesn't scale, i.e. becomes so thin compared to the regular bonds
that it cannot be seen unless one zooms in like mad. Doesn't
matter how wide I ask the pseudo bond to be on the display.

Is there a way to change the preferences for how (thick) pseudo-
bonds are rendered when I save an image using Chimera-rendering?

Sorry to bug you so close to Labor Day weekend but
if you had a quick answer (even if there isn't) that would
help. Alternatively I could maybe draw lines/bonds but
it seems such a pity since the pseudobonds are so beautifully
telling the story on my screen ...

in the worst case, we'll screen shot for now, of course ;-)

Cheers and again I have become a Chimera fan recently
and I am now telling students and coworkers to use it
instead of PyMOL - also because of the amazing tutorials
and help pages. W-O-W !!!


*Elaine, in case you don't remember me - I was a postdoc
with Fred Cohen when you were in Tack's lab in the Midas
days a long long time ago :-)

Dietlind L Gerloff, PhD
Senior Fellow
Foundation for Applied Molecular Evolution (FfAME)
Gainesville, FL 32604
email: dgerloff at ffame.org

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