Dear All,

Thanks for your help!
I amanged to get relion to work without crashing.
FYI, these are the parameters i used
--o Class2D/run1 --i particles_bin2.star --particle_diameter 820
--angpix 2.7 --ctf  --iter 25 --tau2_fudge 2 --K 10 --flatten_solvent
--zero_mask  --strict_highres_exp 10 --oversampling 1 --psi_step 10
--offset_range 5 --offset_step 2 --norm --scale  --j 10

Best,

Pranav

On 9/15/15, HugoMH <[log in to unmask]> wrote:
> Hi Pranav,
>
> I had same problem. If you really want to use particles downsampled, you
> have to normalize with relion_preprocess after particle extraction.
>
> Cheers
>
> Hugo
>
> --
> Hugo Muñoz Hernández, PhD student
>
> Centro de Investigaciones Biológicas CIB-CSIC
> Consejo Superior de Investigaciones Científicas
> C/ Ramiro de Maeztu, 9
> 28040 Madrid (Spain)
>
> http://www.cib.csic.es/es/grupo.php?idgrupo=47
>
> Tel: +34 91 8373112 ext 4436, Lab.B-47
>
>
>
> On 15/09/15 16:15, Fislage, Marcus wrote:
>> Dear Pranav,
>>
>> in the same line to what Celia mentioned.
>> Did you change the pixel size to the double value in the general tab to
>> account for the binning of the data?
>>
>> Cheers
>> Marcus
>>
>>
>> Marcus Fislage, PhD
>>
>> Howard Hughes Medical Institute (HHMI)
>> Columbia University
>> Department of Biochemistry and Biophysics
>> Lab of Joachim Frank
>> New York, NY
>>
>> email address: [log in to unmask]
>> Phone: 212.305.9524
>> Fax: 212.305.9500
>>
>>
>> ________________________________________
>> From: Collaborative Computational Project in Electron cryo-Microscopy
>> [[log in to unmask]] on behalf of Celia Plisson-Chastang
>> [[log in to unmask]]
>> Sent: Tuesday, September 15, 2015 9:58 AM
>> To: [log in to unmask]
>> Subject: Re: [ccpem] Working with downsampled data
>>
>> Hi Pranav,
>>
>> You're right, your 800 (A) diameter mask is too big for  350x350 pixel
>> boxed particles, with a pixel size of 1,35 A.
>> That might explain the script crash.ten switch box
>> do you have a log file to help you find other potential error sources in
>> your script?
>>
>> cheers,
>>
>> Celia
>>
>>
>>
>> Le Mardi 15 Septembre 2015 15:29 CEST, Pranav Shah <[log in to unmask]> a
>> écrit:
>>
>>> Hi Sjors and all,
>>>
>>> I am in the process of performing 2d classification in relion.
>>> I have down-sampled the data to 350px from 700px, normalised the data.
>>>
>>> I have done this via the particle extraction tab. The resulting star file
>>> has also been
>>> saved under particles_binned_350.star.
>>>
>>> Now if i perform 2d classification on the cluster, the job crashes.
>>> My sh file for the cluster looks something like this:
>>>
>>> --o Class2D/run1 -- i particles_binned_350.star --particle_diameter 800
>>> --angpix 1.35 --ctf --tau2_fudge 2 --K10 --flatten_solvent --zero_mask
>>> --strict_highres_exp 10 --oversampling 1 --psi_step 10 --offset_range 5
>>> --offset_step 2 --norm -scale -- j 10 --memory_per_thread 4
>>>
>>> I am not sure why this is happening, but i wonder if it has something to
>>> do with the particle diameter.
>>>
>>> I must also mention that if run class averaging with the unbinned data,
>>> it works to certain extent until the process crashes due to insufficient
>>> memory (but that is a separate issue).
>>>
>>> Looking forward to hearing from you.
>>>
>>> Best,
>>>
>>> Pranav
>> --
>> --
>> Dr Célia Plisson-Chastang
>> Laboratoire de Biologie Moléculaire Eucaryote
>> UMR CNRS 5099-Université Paul Sabatier Toulouse III
>> Bâtiment IBCG, 118 Route de Narbonne
>> 31062 Toulouse Cedex, France
>>
>> Telephone : +33(0)5 61 33 59 50
>> Fax : +33(0)5 61 33 58 86
>
> --
> Hugo Muñoz Hernández, PhD student
>
> Centro de Investigaciones Biológicas CIB-CSIC
> Consejo Superior de Investigaciones Científicas
> C/ Ramiro de Maeztu, 9
> 28040 Madrid (Spain)
>
> http://www.cib.csic.es/es/grupo.php?idgrupo=47
>
> Tel: +34 91 8373112 ext 4436, Lab.B-47
>


-- 
Pranav Shah