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CCPEM  July 2018

CCPEM July 2018

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Subject:

Re: error

From:

Sjors Scheres <[log in to unmask]>

Reply-To:

Sjors Scheres <[log in to unmask]>

Date:

Tue, 3 Jul 2018 11:55:14 +0100

Content-Type:

text/plain

Parts/Attachments:

Parts/Attachments

text/plain (242 lines)

Hi Eric,

It might have been that one of the .gui* files was corrupt. One can
remove these safely from the project directory. If the corruption is
also in one of the saved run.job files in the output directories, then
the problem may return and that specific file should be
removed/repaired. Anyway, happy to see you found a solution yourself.

HTH,

Sjors



On 07/03/2018 08:17 AM, Eric Hanssen wrote:
>
> Well I just answer the question myself …
>
> I created a blank folder, started relion in it, closed it and moved
> all the data from the old folder to the new one, stated relion again
> and it is now all good.
>
> Cheers
>
> Eric
>
>  
>
>  
>
> *-----------------*
>
> *Assoc. Prof Eric Hanssen*
>
> * *
>
> *Head - Advanced Microscopy Facility ***
>
> *Honorary Principal Fellow – Department of Biochemistry and Molecular
> Biology*
>
>
> Bio21 Molecular Science and Biotechnology Institute
> 30 Flemington Road - The University of Melbourne - Victoria 3010 -
> Australia
> email: [log in to unmask] <mailto:[log in to unmask]>|
> Office: +61 3 83442449 | Microscope: +61 3 83442509
>
> Web: www.microscopy.unimelb.edu.au <http://www.microscopy.unimelb.edu.au/>
>
> qqwd
>
>  
>
>  
>
> *From:*Bjoern Forsberg [mailto:[log in to unmask]]
> *Sent:* Tuesday, 3 July 2018 5:04 PM
> *To:* Eric Hanssen; [log in to unmask]
> *Subject:* Re: [ccpem] error
>
>  
>
> This file is a signal to the GUI that the pipeline has changed, hence
> it's not a symptom of a problem as such.
>
> I would advise that you do not use a beta-version for much else than
> testing, especially one that is nearly a year old. There has been many
> fixes since then, and I can see some that pertain to GUI and
> pipelines. Since you seems to have some level of corruption, it might
> not be fixed by updating, but it's nonetheless a good idea.
>
> /Björn
>
> On 2018-07-03 08:36, Eric Hanssen wrote:
>
>     Hi Bjorn,
>
>     Yes I am getting this when I start Relion, hence it actually
>     doesn’t start.
>
>     I am using 2.1-beta1.
>
>     I just noticed that there is .pipeline_has_changed file that I do
>     not have in any other project. I lost the content of the
>     default_pipeline.star last week (in the same hard drive crash) and
>     re-created it from the last job I run following Joshua’s
>     recommendation. I did this for several other project and they are
>     all fine and do not have the .pipeline_has_changed file.
>
>      
>
>     Regards
>
>     Eric
>
>     *-----------------*
>
>     *Assoc. Prof Eric Hanssen*
>
>     * *
>
>     *Head - Advanced Microscopy Facility *
>
>     *Honorary Principal Fellow – Department of Biochemistry and
>     Molecular Biology*
>
>
>     Bio21 Molecular Science and Biotechnology Institute
>     30 Flemington Road - The University of Melbourne - Victoria 3010 -
>     Australia
>     email: [log in to unmask] <mailto:[log in to unmask]>|
>     Office: +61 3 83442449 | Microscope: +61 3 83442509
>
>     Web: www.microscopy.unimelb.edu.au
>     <http://www.microscopy.unimelb.edu.au/>
>
>     qqwd
>
>      
>
>      
>
>     *From:*Collaborative Computational Project in Electron
>     cryo-Microscopy [mailto:[log in to unmask]] *On Behalf Of
>     *Bjoern Forsberg
>     *Sent:* Tuesday, 3 July 2018 4:31 PM
>     *To:* [log in to unmask] <mailto:[log in to unmask]>
>     *Subject:* Re: [ccpem] error
>
>      
>
>     This is often due to using a flag that should be followed by a
>     number, but isn't. But you are getting this when you start up
>     relion? In that case it sounds like a corrupt pipeline. I can't
>     match line 120 to the current version or relion, which version are
>     you using?
>
>     /Björn
>
>      
>
>     On 2018-07-03 06:23, Eric Hanssen wrote:
>
>         Hi all,
>
>          
>
>         After a weird drive crash from last week. all of my projects
>         are back online. However there is one folder I cannot start
>         relion from. The prompt gives me this message:
>
>          
>
>         ERROR:
>
>         Error in textToFloat
>
>         File: /root/relion/src/strings.ccp line: 180
>
>          
>
>          
>
>         Thoughts?
>         regards
>
>         Eric
>
>          
>
>          
>
>          
>
>          
>
>         *-----------------*
>
>         *Assoc. Prof Eric Hanssen*
>
>         * *
>
>         *Head - Advanced Microscopy Facility *
>
>         *Honorary Principal Fellow – Department of Biochemistry and
>         Molecular Biology*
>
>
>         Bio21 Molecular Science and Biotechnology Institute
>         30 Flemington Road - The University of Melbourne - Victoria
>         3010 - Australia
>         email: [log in to unmask]
>         <mailto:[log in to unmask]>| Office: +61 3 83442449 |
>         Microscope: +61 3 83442509
>
>         Web: www.microscopy.unimelb.edu.au
>         <http://www.microscopy.unimelb.edu.au/>
>
>         qqwd
>
>          
>
>          
>
>          
>
>         ------------------------------------------------------------------------
>
>         To unsubscribe from the CCPEM list, click the following link:
>         https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCPEM&A=1
>
>      
>
>      
>
>     ------------------------------------------------------------------------
>
>     To unsubscribe from the CCPEM list, click the following link:
>     https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCPEM&A=1
>
>  
>
>
> ------------------------------------------------------------------------
>
> To unsubscribe from the CCPEM list, click the following link:
> https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCPEM&A=1
>

-- 
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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