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

Elaine Meng meng at cgl.ucsf.edu
Fri Aug 29 15:41:47 PDT 2014

Hi Dietlind,
Of course I remember you!  And thanks for the kind words about Chimera, they mean a lot!

Well, it is a limitation of line rendering… the computer can only draw them up to a certain thickness, and with supersampling (default 3x3) it is trying to make the whole image much larger and then sample it down to the final requested size.  The dialog opened from menu: File… Save Image should report the “effective maximum line width" given its current settings.  That message appears at the bottom of the dialog for several seconds after it’s been opened.

If you are showing the pseudobonds as lines, the only ways to get them a little thicker in the final image is to decrease the final pixel dimensions and/or the amount of supersampling.  When I ran across this issue for journal figures I ended up using 2x2 supersampling, which was quite satisfactory.  You might even try turning off supersampling (1x1) and seeing if the final image is good enough. I agree the limitation is bothersome, however.  It’s mentioned a little bit here:

If that doesn’t give sufficient fatness, however, another possibility is to show the pseudobonds as sticks instead of lines.  You could change them to sticks in the pseudobond attributes opened from the PseudoBond Panel or in the Selection Inspector, or with a command like:

setattr p drawMode 1

(0 is wire, 1 is stick) and adjust radius (again in either of the aforementioned dialogs) or with a command like:

setattr p radius .1

Default radius is 0.2, which might be too fat.  I hope this helps… happy to provide more details or tips if you get stuck!  
Best regards,
Elaine C. Meng, Ph.D.                       
UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab
Department of Pharmaceutical Chemistry
University of California, San Francisco

On Aug 29, 2014, at 3:21 PM, Dietlind Gerloff <dgerloff at ffame.org> wrote:

> 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 !!!
> Dietlind
> *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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