Hi Herman,
There is lots of information on CCP-EM's modelling tools here:
https://www.ccpem.ac.uk/training/icknield_2019/icknield_2019.php
This includes a tutorial on Refmac. As you note this is done in reciprocal space but the CCP-EM pipeline handles conversions from MRC to MTZ format (and runs Refmac via CCP4).
All the best,
Tom
________________________________
From: CCP4 bulletin board <[log in to unmask]> on behalf of Boaz Shaanan <[log in to unmask]>
Sent: 29 July 2020 16:31:46
To: ccp4bb
Subject: Re: [ccp4bb] AW: [EXTERNAL] Re: [ccp4bb] real real-space-refinement
Hi,
Try searching ccp-em.
Boaz
Boaz Shaanan, Ph.D.
Department of Life Sciences
Ben Gurion University of the Negev
Beer Sheva
Israel
On Jul 29, 2020 18:29, "Schreuder, Herman /DE" <[log in to unmask]> wrote:
Coot does it, but if one wants to do it for a complete protein, it is a lot of clicking. On the other hand, I have not tried to just select the N- and C-terminus for real-space refinement to see what happens. I would prefer to have some script to do it.
Best, Herman
Von: Eleanor Dodson <[log in to unmask]>
Gesendet: Mittwoch, 29. Juli 2020 17:23
An: Schreuder, Herman /DE <[log in to unmask]>
Cc: [log in to unmask]
Betreff: [EXTERNAL] Re: [ccp4bb] real real-space-refinement
EXTERNAL : Real sender is [log in to unmask]<mailto:[log in to unmask]>
Wont coot do that?
Eleanor
On Wed, 29 Jul 2020 at 16:20, Schreuder, Herman /DE <[log in to unmask]<mailto:[log in to unmask]>> wrote:
Dear BB,
I would like to do a real real-space-refinement of a protein against a cryo-EM map; not the mtz-based Refmac approach. A quick internet search produced a lot of Phenix hits, but little ccp4 hits. Does somebody know how to do this using ccp4 programs, or has someone a Coot script to do this?
Thank you for your help!
Herman
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