JiscMail Logo
Email discussion lists for the UK Education and Research communities

Help for CCPEM Archives


CCPEM Archives

CCPEM Archives


CCPEM@JISCMAIL.AC.UK


View:

Message:

[

First

|

Previous

|

Next

|

Last

]

By Topic:

[

First

|

Previous

|

Next

|

Last

]

By Author:

[

First

|

Previous

|

Next

|

Last

]

Font:

Proportional Font

LISTSERV Archives

LISTSERV Archives

CCPEM Home

CCPEM Home

CCPEM  September 2018

CCPEM September 2018

Options

Subscribe or Unsubscribe

Subscribe or Unsubscribe

Log In

Log In

Get Password

Get Password

Subject:

Re: Relion 3.0 MotionCor2 Commands

From:

Takanori Nakane <[log in to unmask]>

Reply-To:

Takanori Nakane <[log in to unmask]>

Date:

Mon, 10 Sep 2018 19:55:49 +0100

Content-Type:

text/plain

Parts/Attachments:

Parts/Attachments

text/plain (41 lines)

Hi Colin,

You should put '-Mag x y z' to the "Other MOTIONCOR2 arguments" box
in the "Motion" tab, not the "Additional arguments" box in the
"Running" tab.

The command line to MotionCor2 and its output are written in
(subdirectories of) the job directory as <micrograph_name>.com and
<micrograph_name>.out, respectively.

Note that RELION 3.0 does NOT support anisotropic magnification
correction. This means that the shiny particles after Bayesian
Polishing revert to an uncorrected state. We understand this is a
problem, but the refinement and correction of anisotropic
magnification will be in 3.1, not 3.0.

Best regards,

Takanori Nakane

On 2018/09/10 18:12, Colin K Deniston wrote:
> Hello all,
> 
> 
> I'm a graduate student running MotionCor2 through the new Relion 3.0 GUI and I wish to run with an additional MotionCor2 input for magnification anisotropy ("-Mag x y z"). I can not tell if Relion is actually passing the command through and if MotionCor2 is using the input values. I have tried adding "-Mag x y z" and "--other_motioncor2_args -Mag x y z" in the additional arguments box in the Relion GUI, however I can not tell from any of the files in the output whether Relion successfully passed the command along. Relion has also output "The following warnings were encountered upon command-line parsing: WARNING: Option -Mag  is not a valid RELION argument" both times. Any help in correcting how I input the command and/or where I can look to see that the command was actually passed through to MotionCor2 would be greatly appreciated. Thanks!
> 
> 
> Colin Deniston
> UCSD Graduate Student
> Chemistry and Biochemistry Department
> 
> ########################################################################
> 
> 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

Top of Message | Previous Page | Permalink

JiscMail Tools


RSS Feeds and Sharing


Advanced Options


Archives

September 2018
August 2018
July 2018
June 2018
May 2018
April 2018
March 2018
February 2018
January 2018
December 2017
November 2017
October 2017
September 2017
August 2017
July 2017
June 2017
May 2017
April 2017
March 2017
February 2017
January 2017
December 2016
November 2016
October 2016
September 2016
August 2016
July 2016
June 2016
May 2016
April 2016
March 2016
February 2016
January 2016
December 2015
November 2015
October 2015
September 2015
August 2015
July 2015
June 2015
May 2015
April 2015
March 2015
February 2015
January 2015
December 2014
November 2014
October 2014
September 2014
August 2014
July 2014
June 2014
May 2014
April 2014
March 2014
February 2014
January 2014
December 2013
November 2013
October 2013
September 2013
August 2013
July 2013
June 2013
May 2013
April 2013
March 2013
February 2013


JiscMail is a Jisc service.

View our service policies at https://www.jiscmail.ac.uk/policyandsecurity/ and Jisc's privacy policy at https://www.jisc.ac.uk/website/privacy-notice

Secured by F-Secure Anti-Virus CataList Email List Search Powered by the LISTSERV Email List Manager