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Hi Sjors,
many thanks! I've used the "relion_display" program with parameters
"--lowpass 20 --sigma_contrast 3.0" on the micrographs, and they look as
interpretable as in the picking tasks!
However, it would be _really_ great if RELION's display GUI would offer
such low- and highpass-filtering in all tasks and also in context-based
displays, as in "Show particles from selected classes" and "Show
original image"! This would make all controls and selections by eye much
easier.
Many thanks again, also for such a great software!
Best regards,
Dirk.
On 18.09.2018 14:27, Sjors Scheres wrote:
> Hi Dirk,
>
> The micrographs are low-pass filtered and then displayed, which makes it
> a lot easier to see the particles. You can use --low_pass in
> image_handler to filter particles before displaying.
>
> HTH,
>
> Sjors
>
>
>
> On 09/18/2018 08:46 AM, Dirk Kostrewa wrote:
>> Dear RELION users,
>>
>> I'm working my way through the RELION 3.0beta tutorial and noticed
>> that particles in micrographs are easily recognisable using the
>> "Manual picking" and "Auto-picking" tasks. However, displaying
>> micrographs and extracted particles from other tasks yield mainly
>> grey-on-grey images that are hardly interpretable. Playing with the
>> "Sigma contrast" doesn't really improve the images.
>>
>> I already found this page
>> <https://www2.mrc-lmb.cam.ac.uk/relion/index.php?title=DisplayImages>
>> describing the different image viewers in RELION. My questions are:
>>
>> Can the same settings as in particle picking be applied in other tasks
>> for improved display of micrographs and particles?
>>
>> If not, could you please give me some hints for useful parameters of
>> the relion_image_handler program for getting a good appearance of
>> micrographs and particles?
>>
>> Best regards,
>>
>> Dirk.
>>
>> --
>>
>> **************************************************
>> Dr. Dirk Kostrewa
>> Gene Center Munich
>> Department of Biochemistry, AG Hopfner
>> Ludwig-Maximilians-Universität München
>> Feodor-Lynen-Str. 25
>> D-81377 Munich
>> Germany
>> Phone: +49-89-2180-76845
>> Fax: +49-89-2180-76998
>> E-mail: [log in to unmask]
>> WWW: www.genzentrum.lmu.de
>> **************************************************
>>
>> ------------------------------------------------------------------------
>>
>> To unsubscribe from the CCPEM list, click the following link:
>> https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCPEM&A=1
>>
--
**************************************************
Dr. Dirk Kostrewa
Gene Center Munich
Department of Biochemistry, AG Hopfner
Ludwig-Maximilians-Universität München
Feodor-Lynen-Str. 25
D-81377 Munich
Germany
Phone: +49-89-2180-76845
Fax: +49-89-2180-76998
E-mail: [log in to unmask]
[log in to unmask]
WWW: www.genzentrum.lmu.de
strubio.userweb.mwn.de
**************************************************
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To unsubscribe from the CCPEM list, click the following link:
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