Hi everybody, Thank you very much for the many tips! I discovered that in Coot by clicking on the N- and C-terminus of a protein chain, one can indeed run a real-space refinement on the complete chain and the same is true for a rigid body fit. However, subsequent refinement with Refmac did not converge, so it looks like I still have to go manually through the chains. ☹ Still on my to do list are: - test Isolde - test Main - test the wiggle-fit option in Coot.
Although the Refmac procedure consisting of converting the cryo-EM map into structure factors and running a "crystallographic" refinement on it seems to work, in my opinion the future will be a robust real-space refinement on the cryo-EM map itself, instead of a refinement on derived structure factors. However, this is my personal opinion. Best regards, Herman -----Ursprüngliche Nachricht----- Von: CCP4 bulletin board <CCP4BB@JISCMAIL.AC.UK> Im Auftrag von Tom Burnley - UKRI STFC Gesendet: Mittwoch, 29. Juli 2020 18:51 An: CCP4BB@JISCMAIL.AC.UK Betreff: Re: [ccp4bb] AW: [EXTERNAL] Re: [ccp4bb] real real-space-refinement EXTERNAL : Real sender is owner-ccp...@jiscmail.ac.uk Hi Herman, There is lots of information on CCP-EM's modelling tools here: https://urldefense.proofpoint.com/v2/url?u=https-3A__www.ccpem.ac.uk_training_icknield-5F2019_icknield-5F2019.php&d=DwIFAg&c=Dbf9zoswcQ-CRvvI7VX5j3HvibIuT3ZiarcKl5qtMPo&r=HK-CY_tL8CLLA93vdywyu3qI70R4H8oHzZyRHMQu1AQ&m=aaxzRy8JT0AM0_MqNvU2fr6IB4wIbkY8SsgvQkYcw_w&s=D5VOMK2Fz8AOV1PCvJpD9tm914KUxJlsRNRWXYPb7tI&e= 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 <CCP4BB@JISCMAIL.AC.UK> on behalf of Boaz Shaanan <bshaa...@bgu.ac.il> 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" <herman.schreu...@sanofi.com> 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 <eleanor.dod...@york.ac.uk> Gesendet: Mittwoch, 29. Juli 2020 17:23 An: Schreuder, Herman /DE <herman.schreu...@sanofi.com> Cc: CCP4BB@JISCMAIL.AC.UK Betreff: [EXTERNAL] Re: [ccp4bb] real real-space-refinement EXTERNAL : Real sender is eleanor.dod...@york.ac.uk<mailto:eleanor.dod...@york.ac.uk> Wont coot do that? Eleanor On Wed, 29 Jul 2020 at 16:20, Schreuder, Herman /DE <herman.schreu...@sanofi.com<mailto:herman.schreu...@sanofi.com>> 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! 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