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

[Hannah Bridges]

Hi Greg and Tom,

You make fine points! I was using Chimera-X 0.93 and now I downloaded 
1.1 it can (after a few mins of thinking) open the 70Mb bild files that 
I require  :)

If I run into problems again though now I know that I can submit bug 
reports. I can submit one of these massive files if you wanted to 
optimise the file opening.

Thank you for your help.

Hannah

On 12/01/2021 23:43, Greg Couch wrote:
> HI Hannah,
>
> You didn't say which version of ChimeraX you used.  There was a change 
> just after the 1.0 release that dramatically sped up opening large 
> bild files.   That fix is in the 1.1 release.  But I'm sure there's 
> still room for improvement.  So yes, please report it as a bug and 
> supply the bild file so we can figure what's going wrong in your case.
>
>     -- Greg
>
> On 1/12/2021 10:21 AM, Tom Goddard wrote:
>> 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?
>>
>>     Tom
>>
>>
>>> 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
>>> The Keith Peters Building
>>> University of Cambridge
>>> Cambridge Biomedical Campus
>>> Hills Road
>>> Cambridge
>>> CB2 0XY
>>> United Kingdom
>>>
>>> Telephone : 01223 252812
>>>
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>>
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-- 
Dr Hannah Bridges
Investigator Scientist
MRC Mitochondrial Biology Unit
The Keith Peters Building
University of Cambridge
Cambridge Biomedical Campus
Hills Road
Cambridge
CB2 0XY
United Kingdom

Telephone : 01223 252812