Dear Ezequiel, Be careful, it also happens that the asymmetric contains two half-dimers, with the other half of the dimers being generated by crystallographic operators.
In this case it is not possible to rearrange the monomers such that the asymmetric unit contains one biological dimer and for refinement, one has to stick to the arrangement obtained by molecular replacement. However, for analysis and the making of pictures, it is perfectly valid to generate the two biological dimers using the appropriate crystallographic symmetry operators. WITHIN the dimers generated that way, the monomers will be identical, however, BETWEEN the two dimers, there might be (small) differences, which may or may not be biologically relevant. Good luck! Herman Von: CCP4 bulletin board [mailto:[email protected]] Im Auftrag von Eleanor Dodson Gesendet: Dienstag, 5. März 2019 13:04 An: [email protected] Betreff: [EXTERNAL] Re: [ccp4bb] Change dimer assembly in ASU I tend to use PISA for suggesting biologically relevant complexes. And you can modify the MR solution to replace a molecule with any symmetry generated copy of it.. But check Phaser has put your molecule reasonably close to the origin. On Mon, 4 Mar 2019 at 19:52, Randy Read <[email protected]<mailto:[email protected]>> wrote: Dear Ezequiel, There is nothing special about which particular symmetry copies a molecular replacement program chooses, so there is no good reason to stick to those symmetry copies. On the other hand, there are very good reasons to present a molecule that is as close as possible to what is biologically relevant, so you should definitely change the choices of symmetry copies to make a proper heterodimer in your PDB entry. The easiest way I know to do that is with the option in coot: Extensions->Modelling->Symm Shift Reference Chain Here (after centering on an atom in a symmetry copy that you want to make the master copy). Best wishes, Randy Read ----- Randy J. Read Department of Haematology, University of Cambridge Cambridge Institute for Medical Research Tel: +44 1223 336500 Wellcome Trust/MRC Building Fax: +44 1223 336827 Hills Road E-mail: [email protected]<mailto:[email protected]> Cambridge CB2 0XY, U.K. www-structmed.cimr.cam.ac.uk<https://urldefense.proofpoint.com/v2/url?u=http-3A__www-2Dstructmed.cimr.cam.ac.uk&d=DwMFaQ&c=Dbf9zoswcQ-CRvvI7VX5j3HvibIuT3ZiarcKl5qtMPo&r=HK-CY_tL8CLLA93vdywyu3qI70R4H8oHzZyRHMQu1AQ&m=MDrlBkPs4nOEw_xZLiACGEsL8p0rNBx5dfpYd6zC5Jc&s=1vsmtlsGfw1mW03vAtbqnkRAWzW_K3ioSCxoonFHtxY&e=> > On 4 Mar 2019, at 17:27, Eze Chivi > <[email protected]<mailto:[email protected]>> wrote: > > Dear CCP4bb community: > My crystal is a heterodimeric complex. I solved the structure using MR with a > related structure (containig the dimer), using a highly automated pipeline. > However, the MR solution is not the dimer of biological relevance. The > experimentally validated dimer is formed between a protomer in the ASU and > one from the adjacent symmetry-related pair of molecules. Is it correct to > use a modelling program to assemble the "biologically correct" dimer and then > proceed to refinement? Or... is it need to keep the MR solution and inform in > the PDB header how the relevant dimer is formed? Many Thanks > > Ezequiel > > To unsubscribe from the CCP4BB list, click the following link: > https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB&A=1<https://urldefense.proofpoint.com/v2/url?u=https-3A__www.jiscmail.ac.uk_cgi-2Dbin_webadmin-3FSUBED1-3DCCP4BB-26A-3D1&d=DwMFaQ&c=Dbf9zoswcQ-CRvvI7VX5j3HvibIuT3ZiarcKl5qtMPo&r=HK-CY_tL8CLLA93vdywyu3qI70R4H8oHzZyRHMQu1AQ&m=MDrlBkPs4nOEw_xZLiACGEsL8p0rNBx5dfpYd6zC5Jc&s=PuS4mgiyZmMFSQwR7wkh-tTRSVAVehxN937itHjBnFE&e=> > ######################################################################## To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB&A=1<https://urldefense.proofpoint.com/v2/url?u=https-3A__www.jiscmail.ac.uk_cgi-2Dbin_webadmin-3FSUBED1-3DCCP4BB-26A-3D1&d=DwMFaQ&c=Dbf9zoswcQ-CRvvI7VX5j3HvibIuT3ZiarcKl5qtMPo&r=HK-CY_tL8CLLA93vdywyu3qI70R4H8oHzZyRHMQu1AQ&m=MDrlBkPs4nOEw_xZLiACGEsL8p0rNBx5dfpYd6zC5Jc&s=PuS4mgiyZmMFSQwR7wkh-tTRSVAVehxN937itHjBnFE&e=> ________________________________ To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB&A=1<https://urldefense.proofpoint.com/v2/url?u=https-3A__www.jiscmail.ac.uk_cgi-2Dbin_webadmin-3FSUBED1-3DCCP4BB-26A-3D1&d=DwMFaQ&c=Dbf9zoswcQ-CRvvI7VX5j3HvibIuT3ZiarcKl5qtMPo&r=HK-CY_tL8CLLA93vdywyu3qI70R4H8oHzZyRHMQu1AQ&m=MDrlBkPs4nOEw_xZLiACGEsL8p0rNBx5dfpYd6zC5Jc&s=PuS4mgiyZmMFSQwR7wkh-tTRSVAVehxN937itHjBnFE&e=> ######################################################################## To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB&A=1
