Thanks - yes I think I'll install the latest Relion and re-run the analysis.

Sorry about the cc and large file - will remember for next time!

BW
Sonya

-----Original Message-----
From: Takanori Nakane <[log in to unmask]> 
Sent: 26 January 2022 10:52
To: Sonya James <[log in to unmask]>
Cc: CCPEM <[log in to unmask]>
Subject: Re: [ccpem] Relion convert star

CAUTION: This e-mail originated outside the University of Southampton.

Hi,

 > I was able to produce the particles_3.1.star file  and the pixel size is correct but it doesn't seem to contain the rlnVoltage and rlnSphericalAberration (see attached) so it still wont run the 2D classification.

Apparently your input does not have CTF information.

You should manually add the following items to the optics table.

rlnAmplitudeContrast
rlnSphericalAberration
rlnVoltage

If you are unsure, you should start from the beginning using RELION 3.1 (or 4.0).
Probably it is cleaner and won't take long considering that this is a negative staining dataset.

Also please:

- don't remove CC to CCPEM. Other people cannot benefit from
   this discussion
- don't use screenshots to show texts. Images are larger and hard to search.
   Copy-and-paste as texts.

Best regards,

Takanori Nakane

On 2022/01/26 19:45, Sonya James wrote:
> I was able to produce the particles_3.1.star file  and the pixel size is correct but it doesn't seem to contain the rlnVoltage and rlnSphericalAberration (see attached) so it still wont run the 2D classification.
>
> Thanks
> Sonya
>
> -----Original Message-----
> From: Takanori Nakane <[log in to unmask]>
> Sent: 26 January 2022 09:59
> To: Sonya James <[log in to unmask]>
> Cc: CCPEM <[log in to unmask]>
> Subject: Re: [ccpem] Relion convert star
>
> CAUTION: This e-mail originated outside the University of Southampton.
>
> Hi,
>
> Then convert your Select/jobXXX/particles.star from your subset selection job.
>
> Takanori
>
> On 2022/01/26 18:50, Sonya James wrote:
>> Thanks Takanori,
>>
>> Sorry I should have said - I'm just doing 2D classifications from negative EM staining. I want to select classes from a 2DClass model.star file and run further 2D classification.
>>
>> Many thanks,
>> Sonya
>>
>>
>>
>> -----Original Message-----
>> From: Takanori Nakane <[log in to unmask]>
>> Sent: 26 January 2022 09:25
>> To: Sonya James <[log in to unmask]>; [log in to unmask]
>> Subject: Re: [ccpem] Relion convert star
>>
>> CAUTION: This e-mail originated outside the University of Southampton.
>>
>> Hi,
>>
>> Which step do you want to continue?
>>
>> If you only want to run Refine3D and Class3D, conversion of run_data.star from your previous Refine3D job is sufficient.
>> If you need Polish, you have to convert your movie STAR files as well.
>>
>> The command line syntax is:
>>
>> relion_convert_star --i Refine3D/jobXXX/run_data.star --o 
>> Refine3D/jobXXX/run_data_3.1.star
>>
>> Best regards,
>>
>> Takanori Nakane
>>
>> On 2022/01/26 18:19, Sonya James wrote:
>>> Hello,
>>>
>>> Trying to continue some analysis using Relion 3.1.3 which was originally carried out using Relion 3.0.7. I got the error message:
>>>
>>> ERROR: not all necessary variables defined in _optics.star.file: rlnPixelSize, rlnVoltage and rlnSphericalAberration. Make sure to convert older STAR files anew in version-3.1 with relion convert star.
>>>
>>> How do I do the convert star? Sorry I am a complete novice with Linux so I need step by step instructions!
>>>
>>> Do I have to do it for each .star file individually or can I do all .star files in a directory?
>>>
>>> Thanks for your help,
>>>
>>> Sonya
>>>
>>> ####################################################################
>>> #
>>> #
>>> ##
>>>
>>> To unsubscribe from the CCPEM list, click the following link:
>>> https://eur03.safelinks.protection.outlook.com/?url=https%3A%2F%2Fwww.
>>> jiscmail.ac.uk%2Fcgi-bin%2FWA-JISC.exe%3FSUBED1%3DCCPEM%26A%3D1&amp;
>>> d
>>> a
>>> ta=04%7C01%7Csonya.james%40SOTON.AC.UK%7C6dd84fa5e1f941a7dc6708d9e0a
>>> d
>>> c
>>> 1bd%7C4a5378f929f44d3ebe89669d03ada9d8%7C0%7C0%7C637787859150354227%
>>> 7
>>> C
>>> Unknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik
>>> 1
>>> h
>>> aWwiLCJXVCI6Mn0%3D%7C3000&amp;sdata=uJ%2FTxquv5%2B2xcx1eC5mu6i2FHHhd
>>> y
>>> e
>>> ggTvNcUsZD8nc%3D&amp;reserved=0
>>>
>>> This message was issued to members of 
>>> https://eur03.safelinks.protection.outlook.com/?url=http%3A%2F%2Fwww.
>>> j%2F&amp;data=04%7C01%7Csonya.james%40soton.ac.uk%7C6f38b58e57b9413b
>>> c
>>> 68308d9e0b28910%7C4a5378f929f44d3ebe89669d03ada9d8%7C0%7C0%7C6377878
>>> 7 
>>> 9682939614%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luM
>>> z 
>>> IiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000&amp;sdata=bJgtP1ii%2FMwSLqG9
>>> u
>>> wFu8SzZgNwdMAJIIs%2BecN%2FeSfc%3D&amp;reserved=0
>>> iscmail.ac.uk%2FCCPEM&amp;data=04%7C01%7Csonya.james%40SOTON.AC.UK%7
>>> C
>>> 6
>>> dd84fa5e1f941a7dc6708d9e0adc1bd%7C4a5378f929f44d3ebe89669d03ada9d8%7
>>> C
>>> 0
>>> %7C0%7C637787859150354227%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMD
>>> A
>>> i
>>> LCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000&amp;sdata=UiuA
>>> G s %2FcY4cMfqdBgGG6vqCWwQO2uBGxNFI66F3ALHQ%3D&amp;reserved=0, a 
>>> mailing list hosted by 
>>> https://eur03.safelinks.protection.outlook.com/?url=http%3A%2F%2Fwww.
>>> j%2F&amp;data=04%7C01%7Csonya.james%40soton.ac.uk%7C6f38b58e57b9413b
>>> c
>>> 68308d9e0b28910%7C4a5378f929f44d3ebe89669d03ada9d8%7C0%7C0%7C6377878
>>> 7 
>>> 9682939614%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luM
>>> z 
>>> IiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000&amp;sdata=bJgtP1ii%2FMwSLqG9
>>> u
>>> wFu8SzZgNwdMAJIIs%2BecN%2FeSfc%3D&amp;reserved=0
>>> iscmail.ac.uk%2F&amp;data=04%7C01%7Csonya.james%40SOTON.AC.UK%7C6dd8
>>> 4
>>> f
>>> a5e1f941a7dc6708d9e0adc1bd%7C4a5378f929f44d3ebe89669d03ada9d8%7C0%7C
>>> 0
>>> %
>>> 7C637787859150354227%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJ
>>> Q
>>> I
>>> joiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000&amp;sdata=Q1rKjd2EL
>>> %
>>> 2 FplQxUkXAcdV%2FS4FfQve9YQeKwLRWF8mjk%3D&amp;reserved=0, terms & 
>>> conditions are available at 
>>> https://eur03.safelinks.protection.outlook.com/?url=https%3A%2F%2Fwww.
>>> jiscmail.ac.uk%2Fpolicyandsecurity%2F&amp;data=04%7C01%7Csonya.james
>>> %
>>> 4
>>> 0SOTON.AC.UK%7C6dd84fa5e1f941a7dc6708d9e0adc1bd%7C4a5378f929f44d3ebe
>>> 8
>>> 9
>>> 669d03ada9d8%7C0%7C0%7C637787859150354227%7CUnknown%7CTWFpbGZsb3d8ey
>>> J
>>> W
>>> IjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C300
>>> 0
>>> &
>>> amp;sdata=iy3Bd5%2FV8DdOTyrIkzdEmPINDXoEPWiw%2BiD%2B7YtUj5Q%3D&amp;re
>>> s
>>> erved=0
>>
>

########################################################################

To unsubscribe from the CCPEM list, click the following link:
https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCPEM&A=1

This message was issued to members of www.jiscmail.ac.uk/CCPEM, a mailing list hosted by www.jiscmail.ac.uk, terms & conditions are available at https://www.jiscmail.ac.uk/policyandsecurity/