[Chimera-users] opening large models

Tom Goddard goddard at sonic.net
Thu Mar 17 13:14:20 PDT 2016

Hi Ben,

  It is very likely that you are reading the 80S ribosome structure in mmcif format.  You may not even be aware of this because if you use the command "open 3abc" and the PDB format file is not available because it is a newly deposited structure with more thatn 100,000 atoms or more than 62 chains, the Chimera will automatically fetch the mmCIF version instead (I think this is true for the Chimera daily build).  At any rate, the Chimera mmCIF reader is phenomenally slow and takes extreme amounts of memory.  It is all written in Python by another lab so we are not familiar with the code.  To speed this up you have to read PDB format files instead.  You can download the PDB format files from the PDB web site even for new large structures as a tar gzip archive.  The big structures will be in multiple files PDB format files.

  As Greg said, our next generation ChimeraX will read large mmCIF files very fast, faster than the current Chimera reads PDB format, but ChimeraX is not yet released.


> On Mar 17, 2016, at 12:23 PM, Greg Couch wrote:
> Please use Chimera's Help / Report a Bug dialog to file this as a bug, and, if possible, give the PDB id of the 80S ribosome you are trying to view.  That will tell us about your computer and the size of the structure you're trying to view, and that will enable us to give a better answer.
> So, my guess it that you are trying view a structure that is too big for your computer to handle quickly.  So the solution would be to increase the physical memory.  You may also need a graphics card with more memory.  Another possibility is that you are reading in the structure using the mmCIF reader -- in Chimera, the mmCIF reader is slow and the solution is to use the PDB format version.  Our Chimera successor, ChimeraX, reads mmCIF files very quickly and can     handle large files with ease.  Unfortunately, ChimeraX is not yet available.
>    HTH,
>    Greg
> On 03/17/2016 03:15 AM,  wrote:
>> Hello 
>> Opening a model of the 80S ribosome takes about 30 minutes on my computer (chimera version 1.10.2 build 40686). Is it normal? Is there any way to speed up this step (for example, can the task be parallelized)? 
>> Thanks in advance
>> Ben
>> -- 
>> Prof. Benoît Zuber
>> Institute of Anatomy
>> University of Bern
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>> Switzerland
>> benoit.zuber at ana.unibe.ch <mailto:benoit.zuber at ana.unibe.ch>
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