[Chimera-users] About Chimera under Linux64

Thomas Goddard goddard at cgl.ucsf.edu
Tue Oct 17 09:41:39 PDT 2006

Hi Quentin,

  I suggest you use the 32-bit Linux Chimera version 1.2255.  Or if you
wait a few days a new 32-bit Linux Chimera version 1.2303 will be coming out.

  We do not regularly build a 64-bit Linux Chimera because we do not
have a 64-bit Linux system in our lab.  (I'll have to check on this --
maybe we have one now.)  The only 64-bit version we routinely distribute
is for the very obscure Tru64 operating system running on computers with
Alpha processors.

  The current 64-bit Linux build (May 2005) is so old that it lacks
many useful features for looking at EM maps.

  The reason we have not moved more quickly to support 64-bit distributions
is because Chimera is strongly oriented towards interactive calculations
-- that is calculations taking at most a few seconds.  On gigabyte size
data there is almost nothing that can be done in a few seconds.  Still we
understand that you may look at the data subsampled (using the volume
dialog step size) and then want to create an image at full resolution
(for example for a publication or talk) that may take many minutes to
render and will need alot of memory -- not easily accomodated in a 32-bit
address space.  It is our plan to regularly distribute 64-bit Linux and
Windows version in the future -- probably within a year.  The main hold-up
is that we do not have 64-bit machines setup in our lab yet.

  The usual method of working with large EM tomograms in Chimera is to
focus on smaller regions of interest so that segmentation can be done
interactively.  Practical size chunks of data are 256^3.  You can
select these smaller regions in Chimera.  For large pieces the
graphics hardware is not able to render fast enough to allow smooth
interactive rotation used in segmenting interactively.  It is possible
to display larger volumes and just display every other data plane
along each axis.


> Date: Tue, 17 Oct 2006 14:11:12 +0200
> From: Quentin <derobill at mpi-cbg.de>
> User-Agent: Thunderbird (X11/20060922)
> To: goddard at cgl.ucsf.edu
> Subject: About Chimera under Linux64
> Dear Mr. Goddard,
> I have been setting up the EM tomography in the Max-Planck Institute for
> Molecular Cell Biology and Genetics Dresden (www.mpi-cbg.de Germany )
> since one year. We have a tecnai F30 dedicated for tomogram acquisition
> and it runs after some efforts, with SerialEM/IMOD. I would like to
> improve now the segmentation part of our work which is the bottleneck in
> our fields. So I strive now to get a good set of software to segment and
> visual our huge(600Mb to 6Gb) 3d electron density map (.mrc file format).
> Manfred Auer and Sergio Marco oriented me on your work, i.e. the volume
> data display tools in Chimera. The first tests I did the last days, look
> really promising. Your work is really helpful for the 3D Electron
> Microscopy community. Thanks.
> I am just wondering  why the compiled version for Linux64 of Chimera is
> so old(May 17,2005). Is there some reason? Should I use a newer 32bit
> version ? typically our dataset are 600Mb to 5Gb and we are running a
> dual core Athlon 64 machine with soon 8Gb memory under Ubuntu64bit.
> Thanks for your attention,
> Best regards,
> Quentin de Robillard
> Pfottenhauerstr. 108
> 01307 Dresden
> +49 351 210 20 61

More information about the Chimera-users mailing list