Hi,
First of all, please avoid attaching huge images (9.2 MB!).
A few hundreds pixels are enough to show the map and JPEG compression is
fine. Then the attachment would be less than 1 MB.
Next, please don't drop CC to CCPEM.
> When I generate a mask from this map it looks a bit weird specially for
> the Transmembrane domains (picture attached.)
This is not something unusual.
On the left, your threshold is too high. On the right, your threshold is
too low.
Making a mask for TM regions sometimes needs manual removal of
the micelle before running a Mask Creation job, when no threshold
value can distinguish the TMs from the micelle head groups.
Best regards,
Takanori nakane
On 2022/07/08 9:41, Pinton Tomaleri, Giovani wrote:
> Hi Takanori,
>
> Thanks for getting back to me. It's just puzzling that It is “crunchy”
> at step 1 but at step 2.
>
> When I generate a mask from this map it looks a bit weird specially for
> the Transmembrane domains (picture attached.)
>
> What are your thoughts?
>
> Gio
> ------------------------------------------------------------------------
> *From:* Takanori Nakane <[log in to unmask]>
> *Sent:* Thursday, July 7, 2022 5:31 PM
> *To:* Pinton Tomaleri, Giovani <[log in to unmask]>;
> [log in to unmask] <[log in to unmask]>
> *Subject:* Re: [ccpem] “crunchy” map after 3D auto-refine - RELION-3.1.3
> Hi,
>
> To me the first map looks completely fine but if you are unhappy,
> you might want to tweak the sharpening B factor in PostProcess.
>
> Best regards,
>
> Takanori Nakane
>
> On 2022/07/08 9:08, Pinton Tomaleri, Giovani wrote:
>> Dear CCPEM community,
>>
>> I've imported 195K particles from cryoSPARC and after 3D auto-refine -
>> RELION-3.1.3 I got a map that looks very “pixelated”/“crunchy” (picture
>> 1). Now, If I change the step setting on chimera ( form 1 to 2) the
>> maps look “fine” (picture 2). I am not sure if I am correct, but perhaps
>> one way to overcome this is by resampling it on a finer grid. Is it
>> possible to do it on RELION?
>>
>> Any suggestion would be much appreciated.
>> Gio
>>
>> ------------------------------------------------------------------------
>>
>> To unsubscribe from the CCPEM list, click the following link:
>> https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCPEM&A=1
> <https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCPEM&A=1>
>> <https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCPEM&A=1
> <https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCPEM&A=1>>
>>
########################################################################
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/
|