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

Dietlind Gerloff gerloff at soe.ucsc.edu
Fri Aug 29 15:48:50 PDT 2014

Hi Elaine -

wow you are so fast.. and of course spot on,
those are great ideas, one of them will definitely
do the trick

btw meanwhile I've even used the pov-ray
rendering for those images, funnily they coped
well with these shots (no ribbons shown on them)
and also the overzealous shadowing (which of
course I could change also but i'm lazy) doesn't
bother me in them. with your lovely automation
of the pov-ray they also look so similar in "feel"
to my Chimera-rendered ribbons that I have no
problems at all combining them in the multi-
panel figure I'm creating

Have an absolutely wonderful Labor Day +
thanks so much for the quick reply, I'll
come say hi if/when I hover by at UCSF
next :-)


On Fri, Aug 29, 2014 at 6:41 PM, Elaine Meng <meng at cgl.ucsf.edu> wrote:

> 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:
> <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/print.html#supersampling
> >
> 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
> -----
> 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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