[Chimera-users] Can't open large .bild files

Tom Goddard goddard at sonic.net
Tue Jan 12 10:21:56 PST 2021

Hi Hannah,

  We could look at why Chimera and ChimeraX can't open a 10 Mbyte BILD file if you report a bug using Chimera(X) menu entry Help / Report a Bug... and attach an example file.  Usually BILD files are much smaller than this so it may be nobody ever tried a file that large.  I'm guessing it is not a memory limitation.  More likely it is some O(n**2) behavior of the reader, in other words if you have N points or line or arrows in the file it is coded poorly and taking N*N operations to read it.  A clue to that could be deduced if you have BILD files of different sizes that do open, how long in seconds do files of different sizes take to open?


> On Jan 12, 2021, at 9:52 AM, Hannah Bridges <hrb at mrc-mbu.cam.ac.uk> wrote:
> Thanks Elaine,
> I tried that but unfortunately it didn't help . What is odd to me is that both chimera and chimerax can open mrc/ccp4 files that are substantially larger without too much trouble.
> Best wishes
> Hannah
> On 05/01/2021 19:37, Elaine Meng wrote:
>> Hi Hannah,
>> I do not know the answer to your question, but suggest trying ChimeraX instead of Chimera.  ChimeraX reads the same bild format and is generally much better with large data.
>> <https://www.rbvi.ucsf.edu/chimerax/>
>> <https://www.rbvi.ucsf.edu/chimerax/download.html>
>> <https://rbvi.ucsf.edu/chimerax/docs/user/formats/bild.html>
>> I hope this helps,
>> Elaine
>> -----
>> Elaine C. Meng, Ph.D.
>> UCSF Chimera(X) team
>> Department of Pharmaceutical Chemistry
>> University of California, San Francisco
>>> On Jan 5, 2021, at 6:23 AM, Hannah Bridges <hrb at mrc-mbu.cam.ac.uk> wrote:
>>> Hi all,
>>> I would like to visualize in Chimera the orientations from some angdist.bild files output from relion. I am able to open some .bild files (up to ~5.6MB in size) but I get "not responding" from Chimera when I try to open .bild files ~10-70MB (lots of particles and high angular sampling). I tried on a machine with more RAM but it was the same. Any hints about how to open these or is it just not possible?
>>> Best wishes
>>> Hannah
> -- 
> Dr Hannah Bridges
> Investigator Scientist
> MRC Mitochondrial Biology Unit
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