Hi Dieter,
You can try bigger groups and see whether that works. The new Display
program makes this easier: after clicking the big red Display button on
the main GUI select the last iteration model.star file from your
classification run. Then, on the small display options window select the
"Group particles" line at the bottom and provide a reasonable number of
groups, e.g. 20 or 50. Then, when you save the STAR file with the
particles from the selected classes (right mouse popup menu in the display
window of the classes), the new STAR file will have the
requested number of groups. This procedure replaces the more cumbersome
shell scripts for grouping in release 1.2
HTH,
S
> Hi Sjors,
> thanks! I run it on a PC with 4 CPUs, so I do not believe that it
> might be harware-related (or maybe yes?). I also continued the run and
restarted from scratch as well (each time with somewhat different CTF
groups). The error then occurred at different iterations but it never
ran until convergence. Do you have a suggestion of what I might try? I
should say that 3D-refinement using the entire data set (without prior
3D-classification) ran until convergence.
> Best, Dieter
> ------------------------------------------------------------------------
Dieter Blaas,
> Max F. Perutz Laboratories
> Medical University of Vienna,
> Inst. Med. Biochem., Vienna Biocenter (VBC),
> Dr. Bohr Gasse 9/3,
> A-1030 Vienna, Austria,
> Tel: 0043 1 4277 61630,
> Fax: 0043 1 4277 9616,
> e-mail: [log in to unmask]
> ------------------------------------------------------------------------
Am 07.07.2014 09:51, schrieb Sjors Scheres:
>> Hi Dieter,
>> Did any of the numbers in the model.star file go NaN before crashing at
iteration 16? Otherwise, perhaps there was something a hardware glitch
and
>> some MPI message didn't arrive well. Did you try just re-starting from
iteration 16?
>> HTH,
>> S
>>> Dear Sjors,
>>> I ran a 3D-classification into 2 classes until iteration 25
without
>>> problems. I then extracted the particle images corresponding to the
respective classes, made CTF groups containing not less than 20
particles per group and ran 3D-Refinements on both classes without
problems up to iteration 16 for one and iteraction 6 for the other
class. I then received the error message:
>>> Expectation iteration 16
>>> 0.08/2.18 min ..~~(,_,"> exp_thisparticle_sumweight=
>>> nan [$
>>> exp_part_id= 2039exp_iimage=1
>>> group_id= 61 mymodel.scale_correction[group_id]= 1.14594
>>> exp_ipass= 0
>>> sampling.NrDirections(0, true)= 48 sampling.NrDirections(0, false)=
>>> 16
>>> sampling.NrPsiSamplings(0, true)= 96 sampling.NrPsiSamplings(0,
>>> false)=
>>> 6
>>> mymodel.sigma2_noise[exp_ipart]=
>>> I tried various ways to group the particles but always ran into
>>> similar problems. Should I make the groups bigger, say 40 or 50 particle
>>> images per group or even more? Or what is wrong with group 61? Thanks
a lot, best, Dieter
>>> ------------------------------------------------------------------------
Dieter Blaas,
>>> Max F. Perutz Laboratories
>>> Medical University of Vienna,
>>> Inst. Med. Biochem., Vienna Biocenter (VBC),
>>> Dr. Bohr Gasse 9/3,
>>> A-1030 Vienna, Austria,
>>> Tel: 0043 1 4277 61630,
>>> Fax: 0043 1 4277 9616,
>>> e-mail: [log in to unmask]
>>> ------------------------------------------------------------------------
--
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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