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CCPEM  April 2016

CCPEM April 2016

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Subject:

Re: Relion: pdf_offset error

From:

Sjors Scheres <[log in to unmask]>

Reply-To:

Sjors Scheres <[log in to unmask]>

Date:

Thu, 14 Apr 2016 13:38:15 +0100

Content-Type:

text/plain

Parts/Attachments:

Parts/Attachments

text/plain (78 lines)

Hi Reza,
Your interpretation is correct. The numbering that Juha mentioned though 
was the index from a vector inside RELION, so not directly related to 
the particle rlnImageName in the STAR file. In fact, at that point in 
the code, RELION doesn't have access to the complete STAR file (for 
memory efficiency reasons).
S

On 04/14/2016 01:14 PM, Reza Khayat wrote:
> Hi Sjors,
>
> I'm a bit confused here. I was under the impression that particle star entries tell Relion what particles to read; thus, removing an entry would not tell Relion what particles to read. For example,
>
> .....   [log in to unmask] ...
> .....   [log in to unmask] ...
> .....   [log in to unmask] ...
>
> tells Relion to read particles 1, 3 and 4 from the stack Micrograph001_particles.mrcs. Is this an incorrect interpretation of how the program works?
>
> Best wishes,
> Reza
>
> Reza Khayat, PhD
> Assistant Professor
> Department of Chemistry
> City College of New York
> 85 Saint Nicholas Terrace, CDI 2.318
> New York, NY 10031
> http://www.khayatlab.org/
> 212-650-6070
>
> -----Original Message-----
> From: Collaborative Computational Project in Electron cryo-Microscopy [mailto:[log in to unmask]] On Behalf Of Sjors Scheres
> Sent: Thursday, April 14, 2016 7:53 AM
> To: [log in to unmask]
> Subject: Re: [ccpem] Relion: pdf_offset error
>
> Hi Juha,
> Yes, these things sometimes happen with odd particles. Does the sorting reveal anything odd? Or a simple analysis of statistics?
> The numbering gets randomised, I'm afraid.
> S
> On 04/14/2016 09:31 AM, Juha Huiskonen wrote:
>> Dear Sjors and Relion users,
>>
>> I am encountering the following error during 3D classification:
>>
>> pdf_offset= 0 pdf_orientation= 0.0037792    [oo]
>>    ipart= 0 part_id= 2718
>>    iorient= 0 idir= 0 ipsi= 0
>>    exp_directions_prior[0]= 1
>>    exp_psi_prior[0]= 0.0037792
>> ...
>>    exp_psi_prior[9]= 0.00601489
>> ERROR! pdf_offset==0.|| pdf_orientation==0.
>> File: src/ml_optimiser.cpp line: 4130
>>
>> It seems particle number 2718 is somehow bad. Should I simply remove
>> the 2718th line from the star file? Does numbering start from 0 or 1?
>> (I might be missing something as I tried both. As it didn't work I
>> suspect the numbering is not sequential somehow.)
>>
>> Best wishes,
>> Juha
>>
> --
> 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

-- 
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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