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. Tom
Date: Tue, 17 Oct 2006 14:11:12 +0200 From: Quentin <derobill@mpi-cbg.de> User-Agent: Thunderbird 1.5.0.7 (X11/20060922) To: goddard@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