Hello, have you tried anisotropic B-factor refinement? It is usually very good at cleaning-up the difference map. At that sort of resolution, you may still have some way to go in the refinement since the R and R-free usually go to about half of what you have, at least with proteins.
Best wishes, Jon Cooper. jon.b.coo...@protonmail.com -------- Original Message -------- On 29 Jul 2020, 14:56, Eleanor Dodson wrote: > Sometimes ghost like this mean there is a spacegroup error - absences can be > the result of the non-crystallographic translation and not be truly > indicitive of the spacegroup. > what is the possible spacegroup and what is the NC translation vector? > Eleanor > > On Wed, 29 Jul 2020 at 14:13, Schreuder, Herman /DE > <herman.schreu...@sanofi.com> wrote: > >> Dear Rafal, >> >> At this resolution, one sees many amino-acid side chains with alternative >> conformation, so it might be a good idea to test if this is also true for >> nucleotides. >> >> Best, Herman >> >> -----Ursprüngliche Nachricht----- >> Von: CCP4 bulletin board <CCP4BB@JISCMAIL.AC.UK> Im Auftrag von Rafal Dolot >> Gesendet: Mittwoch, 29. Juli 2020 14:42 >> An: CCP4BB@JISCMAIL.AC.UK >> Betreff: [EXTERNAL] [ccp4bb] Problems with refinement of nucleic acid >> structure >> >> EXTERNAL : Real sender is owner-ccp...@jiscmail.ac.uk >> >> Dear CCP4 users, >> >> I'm working on the another nucleic acid duplex structure. After several >> stages of rebuilding and refinement I observed something like a "shadow" >> of the second duplex position. Have you any ideas to explain this phenomena? >> Should I place the second molecule with occupancy completed to the first >> one? Or maybe is it a kind of disorder in crystal lattice? >> Data were collected to 1.02A using synchrotron radiation (processed with >> XDS), but I have another datasets collected to lower resolution (from >> Zn-SAD) with visible similar effects. Refinement was done using Refmac >> (R/Rfree 21.5/24.0). Data not appeared to be twinned, but Xtriage detected >> pseudo-translational symmetry. >> >> Thank you for any advices. >> >> Rafal >> >> |----------------------------------------------| >> |Rafal Dolot, Ph.D. | >> | | >> |Polish Academy of Sciences | >> |Centre of Molecular and Macromolecular Studies| >> |Department of Bioorganic Chemistry | >> |Macromolecular Crystallography Team | >> |Sienkiewicza 112 | >> |90-363 Lodz, Poland | >> |Phone: +48(42)6803215 | >> |Cell: +48 502897781 | >> |----------------------------------------------| >> >> ######################################################################## >> >> To unsubscribe from the CCP4BB list, click the following link: >> https://urldefense.proofpoint.com/v2/url?u=https-3A__www.jiscmail.ac.uk_cgi-2Dbin_WA-2DJISC.exe-3FSUBED1-3DCCP4BB-26A-3D1&d=DwICAg&c=Dbf9zoswcQ-CRvvI7VX5j3HvibIuT3ZiarcKl5qtMPo&r=HK-CY_tL8CLLA93vdywyu3qI70R4H8oHzZyRHMQu1AQ&m=cDOmaUoERSX6Rz_GQvd1VxncHBGPvEnDlYJSypA0P-M&s=bxs7KYSqKDM2UBAguUYP_9utSJpoMdJ0N3qRJOBQ1v0&e= >> >> This message was issued to members of >> https://urldefense.proofpoint.com/v2/url?u=http-3A__www.jiscmail.ac.uk_CCP4BB&d=DwICAg&c=Dbf9zoswcQ-CRvvI7VX5j3HvibIuT3ZiarcKl5qtMPo&r=HK-CY_tL8CLLA93vdywyu3qI70R4H8oHzZyRHMQu1AQ&m=cDOmaUoERSX6Rz_GQvd1VxncHBGPvEnDlYJSypA0P-M&s=dJtlr7D5BN24QQ-TBSNysQi31jIrarcnXWm4TpREHf0&e=, >> a mailing list hosted by >> https://urldefense.proofpoint.com/v2/url?u=http-3A__www.jiscmail.ac.uk&d=DwICAg&c=Dbf9zoswcQ-CRvvI7VX5j3HvibIuT3ZiarcKl5qtMPo&r=HK-CY_tL8CLLA93vdywyu3qI70R4H8oHzZyRHMQu1AQ&m=cDOmaUoERSX6Rz_GQvd1VxncHBGPvEnDlYJSypA0P-M&s=61QRZ35Nd2knlHLbWpFLGGUD_aa18yIOsQtLlDQwcXo&e=, >> terms & conditions are available at >> https://urldefense.proofpoint.com/v2/url?u=https-3A__www.jiscmail.ac.uk_policyandsecurity_&d=DwICAg&c=Dbf9zoswcQ-CRvvI7VX5j3HvibIuT3ZiarcKl5qtMPo&r=HK-CY_tL8CLLA93vdywyu3qI70R4H8oHzZyRHMQu1AQ&m=cDOmaUoERSX6Rz_GQvd1VxncHBGPvEnDlYJSypA0P-M&s=sNhiuaGAxt8e9Fhizzcy4JHfAFv4fAW-8tUFxrYZDmk&e= >> >> ######################################################################## >> >> To unsubscribe from the CCP4BB list, click the following link: >> https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1 >> >> This message was issued to members of www.jiscmail.ac.uk/CCP4BB, a mailing >> list hosted by www.jiscmail.ac.uk, terms & conditions are available at >> https://www.jiscmail.ac.uk/policyandsecurity/ > > --------------------------------------------------------------- > > To unsubscribe from the CCP4BB list, click the following link: > https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1 ######################################################################## To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1 This message was issued to members of www.jiscmail.ac.uk/CCP4BB, a mailing list hosted by www.jiscmail.ac.uk, terms & conditions are available at https://www.jiscmail.ac.uk/policyandsecurity/
