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  March 2015

CCPEM March 2015

Options

Subscribe or Unsubscribe

Subscribe or Unsubscribe

Log In

Log In

Get Password

Get Password

Subject:

Re: Flexibility

From:

Sjors Scheres <[log in to unmask]>

Reply-To:

Sjors Scheres <[log in to unmask]>

Date:

Sun, 1 Mar 2015 09:56:47 -0000

Content-Type:

text/plain

Parts/Attachments:

Parts/Attachments

text/plain (103 lines)

Hi Remi,
In relion-1.4 this will be easier: you can just start an autorefine from
local searches. In relion-1.3, you need to restart an old run from some
intermediate iteration and modify the model and optimiser.star files of
that iteration to provide the other mask. Just change the value for the
lab with the solvent mask.
HTH,
S

> Dear Sjors,
>
> Thank you very much for your reply.
> I am currently trying something like that. I ran an auto-refine on the
> whole particle. Then I defined a 3D mash around only one of the two
> domains. Then I continued the auto-refine providing this mask to further
> refine this domain only. However, it is not clear to me what option to use
> in relion_refine to force it to continue auto-refine using local search
> only.
>
> Thanks for your help
>
> All the best
>
>
> Rémi Fronzes
> G5 biologie structurale de la sécrétion bactérienne, institut Pasteur
> CNRS UMR 3528, institut Pasteur
>
> Office: +33 (0)145688864
> Lab: +33 (0) 145688863
> Mobile: +33 (0) 688263992
> Email: [log in to unmask] <mailto:[log in to unmask]>
>
> 25 rue du Docteur Roux
> Bâtiment Metchnikoff, 3ème étage
> 75015 Paris, France
>
>> Le 26 févr. 2015 à 09:16, Sjors Scheres <[log in to unmask]> a
>> écrit :
>>
>> Dear Remi,
>> Currently, one would have to do masked refinements of both domains
>> separately (and somehow keep them from mixing up by using local
>> searches).
>> Ongoing work will try to deal with this in a better way, but this
>> project
>> will probably take a while...
>> HTH,
>> S
>>
>>
>>> Dear All,
>>>
>>> Let’s say a protein complex is composed of two domains liked by a
>>> flexible linker. Is there a way to refine each domain independently in
>>> relion ?
>>> For example, if I provide only domain 1 as staring model, will it push
>>> relion to refine this domain over the other ? (given that the two
>>> domains
>>> have sufficiently distinct structures)
>>>
>>> Thanks
>>>
>>> All the best
>>>
>>> Rémi
>>>
>>>
>>> Rémi Fronzes
>>> G5 biologie structurale de la sécrétion bactérienne, institut
>>> Pasteur
>>> CNRS UMR 3528, institut Pasteur
>>>
>>> Office: +33 (0)145688864
>>> Lab: +33 (0) 145688863
>>> Mobile: +33 (0) 688263992
>>> Email: [log in to unmask] <mailto:[log in to unmask]>
>>>
>>> 25 rue du Docteur Roux
>>> Bâtiment Metchnikoff, 3ème étage
>>> 75015 Paris, France
>>>
>>>
>>
>>
>> --
>> Sjors Scheres
>> MRC Laboratory of Molecular Biology
>> Francis Crick Avenue, Cambridge Biomedical Campus
>> Cambridge CB2 0QH, U.K.
>> tel: +44 (0)1223 267061
>> http://www2.mrc-lmb.cam.ac.uk/groups/scheres
>
>


-- 
Sjors Scheres
MRC Laboratory of Molecular Biology
Francis Crick Avenue, Cambridge Biomedical Campus
Cambridge CB2 0QH, U.K.
tel: +44 (0)1223 267061
http://www2.mrc-lmb.cam.ac.uk/groups/scheres

Top of Message | Previous Page | Permalink

JiscMail Tools


RSS Feeds and Sharing


Advanced Options


Archives

October 2018
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