Hi Sjors,

Thanks! I would like to use the newer version. Unfortunately the installation doesn't work in our system at this point.
We are actively working on the problem and hopefully it will  work soon.

Best,

Zongli
________________________________________
From: Sjors Scheres [[log in to unmask]]
Sent: Monday, October 20, 2014 11:57 AM
To: Li, Zongli
Cc: [log in to unmask]
Subject: Re: [ccpem] Error when run 3D auto-refine

The regrouping using the display will only work in 1.3. In 1.2 this was
still done using shell scripts. If you are still using relion-1.2, I
would definitely recommend updating to 1.3. I guarantee you will like
the 1.3 GUI better than the 1.2 one. If not, I will return you your
money! ;-)
HTH,
S
On 10/20/2014 04:25 PM, Li, Zongli wrote:
> Hi Sjors,
>
> Thanks a lot. Yes, I did see the warnings at the beginning of 3D classification.
>
> When displaying the model.star, do I have to use relion 1.3 instead of 1.2?
>
> Best,
>
> Zongli
> ________________________________________
> From: Sjors Scheres [[log in to unmask]]
> Sent: Monday, October 20, 2014 11:23 AM
> To: Li, Zongli
> Cc: [log in to unmask]
> Subject: Re: [ccpem] Error when run 3D auto-refine
>
> Hi Zongli,
> The scale correction for group 941 gave a value very far from 1
> (12838.3). Are there enough particles in the selected subset of
> particles for each group? If not, the program will write out warnings at
> the beginning of the run, and you may experience this type of behaviour.
> The solution then lies in grouping multiple micrographs together. This
> can be done conveniently when displaying the model.star from the
> previous 3D classification run. Just tick the option to "regroup
> selected particles in number of groups", and provide a reasonable
> number, e.g. 50 or 100.
> HTH,
> S
>
> On 10/20/2014 03:56 PM, Li, Zongli wrote:
>> Hi Sjors,
>>
>> I have been doing 3D classification and 3D auto-refine using Relion 1.2. The  job was submitted in command line.
>> The 3D classification run smoothly to the end without any problems. However, the 3D auto-refine for one of the classes
>> got stuck at iteration 11. The job was running on a linux cluster that using LSF system. When check with "bjobs", the job
>>    is running fine, but no any progress for 6 days. Here is the error message:
>>
>>    The following warnings were encountered upon command-line parsing:
>> WARNING: Option --dont_combine_weights_via_disc is not a valid argument
>>    rlnMicrographScaleCorrection= 12838.3 group= 941 my_image_no= 0
>> ERROR: rlnMicrographScaleCorrection is very high. Did you normalize your data?
>> File: src/ml_optimiser.cpp line: 4271
>>
>> I did normalize my data. Do you know what is the problem and how to fix it?
>>
>> Thanks a lot!
>>
>> Zongli
> --
> 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