[Chimera-users] opening large models

benoit.zuber at ana.unibe.ch benoit.zuber at ana.unibe.ch
Thu Mar 17 14:50:13 PDT 2016


Hi Tom and Greg,
Indeed the problem was that I was opening an mmCIF file. It was not saturating the RAM but only very slow to open. I now found the corresponding pdb bundle, each file of which opened in less than 1 second. Many thanks for your suggestions!
Ben


________________________________
Von: Tom Goddard [goddard at sonic.net]
Gesendet: Donnerstag, 17. März 2016 21:14
An: Zuber, Benoît (ANA)
Cc: Chimera User Forum
Betreff: Re: [Chimera-users] opening large models

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.

Tom


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
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