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CCPEM  July 2018

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Subject:

Re: tilted collect ctf estimation in relion

From:

Kai Zhang <[log in to unmask]>

Reply-To:

[log in to unmask]

Date:

Tue, 10 Jul 2018 13:30:04 +0100

Content-Type:

text/plain

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text/plain (80 lines)

Hi Chiara,

There several parameters you might try to improve for a specific dataset.
--local_radius    1024.00   default value seems a bit too big, though more
stable. For micrographs with better SNR, try to reduce this weighting
radius.
--local_overlap   0.50      larger value, say 0.8, is always better, but
the speed is slower.
--local_boxsize   512       300-800 all seem to work OK in most cases, but
do try to see which works best.
--write_local_ctf           specify it for diagnosis, not necessary for
batch processing.

P.S. Note the current local power spectra weighting scheme and local CTF
refinement strategy implemented in GCTF was >4 years old. Though I believe
it works well in most cases, there is always some room to make it better
and things have been slightly improved in many aspects in the newer
versions. I will release it at some point when I settle down in US.

Best wishes
Kai

> Hi Chiara,
> You don't have to convert your particle into .box format. Simply specify
_autopick.star for the --boxsuffix. I would first link all the
micrographs
> into the folder that contains the particle coordinates that you have
picked in RELION. In my case, it is the folder
Autopick/job010/micrographs
> .
> Here is an example command line:
> Gctf-v1.06_sm_20_cu8.0_x86_64 *.mrc  --do_local_refine --boxsuffix
_autopick.star --apix 1 --kV 300 --Cs 2.7
> Hope it answers your question.
> Best,
> Chen
> ________________________________
> From: Collaborative Computational Project in Electron cryo-Microscopy
<[log in to unmask]> on behalf of Chiara Rapisarda
> <[log in to unmask]>
> Sent: Monday, July 9, 2018 1:05:57 PM
> To: [log in to unmask]
> Subject: [ccpem] tilted collect ctf estimation in relion
> Hello,
> I have just collected a series of 40 deg tilted micrographs and I would
like to do a per particle CTF estimation in RELION 2.1 (as I used to do
on
> EMAN2). I couldn’t find a thread where the topic was discussed. Is it
even
> possible, and if not, are there any other options ? Would it work by
command line?
> I found this command: Gctf-v0.50_sm_30_cu5.0_x86_64
> Micrographs/Falcon*.mrc --do_EPA --apix 1.07 --do_local_refine
--boxsuffix
> .box
> I have autopicked particles on relion, would I be able to use this
command
> if I convert my particles into a .box format?
> Thank you for any help,
> Chiara
> Chiara Rapisarda
> Post doc
> Université de Bordeaux, CNRS, INSERM
> [log in to unmask]
> Tel. +33 (5) 4000 3617
> Institut européen de chimie et biologie
> 2, rue Robert Escarpit
> 33607 Pessac, France
> www.iecb.u-bordeaux.fr
> ________________________________
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