[Chimera-users] Using the modeldisp command

Forbes J. Burkowski fjburkow at plg.uwaterloo.ca
Tue Feb 7 16:23:29 PST 2012

Thanks for looking into this.

By the way, I just happened to chance upon the Protein Data Bank page in


If you go down to the section on "Viewing the data" there is a lengthy
list of molecular display programs including Chimera.  They all have links
to the homepages except for UCSF Chimera!

This nasty omission should be corrected as soon as possible.


On Tue, 7 Feb 2012, Eric Pettersen wrote:

> On Feb 7, 2012, at 1:07 PM, Forbes J. Burkowski wrote:
> > This VRML snippet gives me an array of 100 little cubes. Here's the
> > catch:
> >
> > On last year's version of Chimera (1.5.3) the script generates the
> > scene
> > almost instantaneously. With the current version of Chimera (the
> > January
> > release or the Feb. 04 release) the execution is extremely slow.  I am
> > running Windows 7 on a machine with 12 GB of RAM and an Intel i7 CPU
> > 3.2GHz so I am not lacking for computing power.  One of my students
> > also
> > tried this script and reports a similar slow down.
> Urg.  You're right; whereas it takes a couple of seconds to open on
> 1.5.3, it takes basically forever on 1.6.  I'll be opening a ticket in
> our bug database about this with you on the recipient list so you'll
> know when it is fixed.  I hope it gets fixed in time for the 1.6 final
> version but if not then it will be fixed in 1.6.1 for sure.
> > I am also noticing
> > that the latest version seems to launch more slowly and takes more
> > time to
> > display BIG scenes (consider PDB ID = 1FFK).
> Well, this is actually a side effect of the VRML thing.  I hadn't
> anticipated the direct opening of VRML strings when writing the new
> Rapid Access interface.  Consequently, the text of one of the
> "recently opened" buttons is the entirety of the VRML string you
> opened!  It actually only shows the last two curly braces, LOL.  At
> any rate, showing that huge VRML string on the button is causing all
> the slowdown.
> I have committed a fix for this latter problem and it will be in the
> next successful build.  If the slowness is bugging you too much to
> wait you could go and edit ~/.chimera/preferences, search for "Rapid
> Access", find the first opening curly brace after it (start of a
> dictionary) and change the 'data history' list to an empty list.
> Thanks for reporting this, BTW.
> --Eric
>                          Eric Pettersen
>                          UCSF Computer Graphics Lab
>                          http://www.cgl.ucsf.edu

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