It will even depend on the signal-to-noise ratios in the images and the
shape of your protein. So it is VERY hard to predict.
HTH,
Sjors
On 11/20/2015 03:15 PM, Martyn Winn wrote:
> Hi,
>
> I started collating some timings at http://www.ccpem.ac.uk/user_help/relion_benchmarks.php for auto-refine.
>
> Big caveat: will depend a lot on compute hardware, number of nodes/threads, size of structure, version of Relion, chosen precision, etc etc. So I am a little nervous to advertise this, as it is only one possible answer ... I agree the Elife paper is good.
>
> HTH
> Martyn
>
> From: Collaborative Computational Project in Electron cryo-Microscopy [mailto:[log in to unmask]] On Behalf Of Ludovic Renault
> Sent: 20 November 2015 14:54
> To: [log in to unmask]
> Subject: Re: [ccpem] RELION 3D classification and 3D autorefine
>
> Hi Joshua,
> There's a nice Elife paper that looked into that. It's cloud computing but will still give you an idea.
> http://elifesciences.org/content/4/e06664
> I would suggest to do a few tests as each cluster is different.
> Ludo
>
> On Fri, Nov 20, 2015 at 2:41 PM, Joshua Lobo <[log in to unmask]<mailto:[log in to unmask]>> wrote:
> Hi everyone
>
>
> I have a question regarding the average time of a run of 3D classification and auto-refine . Is there any formula or rule of thumb to make a rough estimate of how much time the job will take to say run 1 iteration ? Also how many processors and how much RAM is norrmally used for the 3D classification and autorefine . I'm looking to get the most out of my cluster so these parameters will and timing info will really help.
>
>
> Sincerely
>
> Joshua Lobo
>
--
Sjors Scheres
MRC Laboratory of Molecular Biology
Francis Crick Avenue, Cambridge Biomedical Campus
Cambridge CB2 0QH, U.K.
tel: +44 (0)1223 267061
http://www2.mrc-lmb.cam.ac.uk/groups/scheres
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