Print

Print
Hi Chiara, 

Given that you’ve collected tilted single-particle data, you might be interested in alternative approaches to estimating the CTF. What we know is that the focus gradient is still an issue, and a source of error for tilted data (especially at 40°), but in principle, this error can be reduced with more accurate methods for estimating the CTF. We’ve recently started using Warp for CTF estimation, which for some cases, we find provides better results than the per-particle estimation implemented in GCTF. We don’t yet have many data points, but the results presented in the manuscript, specifically the improvements with patch-based CTF estimation, are pretty convincing. We have also had an improvement with one particular case. 

Hope this helps,

Dmitry

 


On Jul 9, 2018, at 10:18 AM, Chen Sun <[log in to unmask]> wrote:

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


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

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


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