Hi Daniele, I agree with Wim that the first thing you should check is your space group and especially whether a ncs symmetry element has been mistakenly identified as being crystallographic. Since your Patterson peak is along w (c-axis), you have to change the space group for processing such, that there are no rotation axes or other symmetry elements perpendicular to the c-axis any more. If you have a low-symmetry space group, you could also process in P1 to be absolutely on the safe side. Than you should run MR in this lower symmetry space group.
Concerning lattice translocation defects, almost every case is unique and I am not aware of any software able to handle this. Here you will have to work out the maths for your particular case yourself and apply the correction with e.g. sftools. I am a little puzzled by your 7Å vector in your (native?) Patterson maps. I guess, if you translate your protein by 7Å it will strongly overlap with itself and I guess the same will be true for your ghost map. You should also have a look at your diffraction images, perhaps after summing them to 1° slices so become human-interpretable. In many cases, LTD is associated with a mix of sharp and fuzzy diffraction spots. Seeing those would be a strong indicator that you have the problem, but there are cases of LTD where all the spots are sharp. You may also want to check for statistical disorder. Good luck! Herman Von: CCP4 bulletin board <CCP4BB@JISCMAIL.AC.UK> Im Auftrag von Wim Burmeister Gesendet: Mittwoch, 12. Februar 2020 08:57 An: CCP4BB@JISCMAIL.AC.UK Betreff: [EXTERNAL] Re: [ccp4bb] Lattice-translocation defect (LTD) EXTERNAL : Real sender is owner-ccp...@jiscmail.ac.uk<mailto:owner-ccp...@jiscmail.ac.uk> Hello, do you have some details about the space group ? Did the integration not miss any sports ? I would rather think of an ncs close to crystallographic symmetry, or maybe some twinning problem. I guess these are Pilatus data, can you combine the frames into 1 degree oscillations and try Mosflm processing to see how the patterns integrate ? Greetings Wim Le 11/02/2020 à 22:31, Daniele de Sanctis a écrit : Hi all, I'm currently dealing with what I think it is a case of LTD (off-origin Patterson peak, with vector along w of ~ 7A and electron density map showing a "ghost" map shifted by 7 A). I saw there are quite a few cases reported in literature (for example Hare et al, 2006), but what I could not find is how I can demodulate the data. Is there any software that can be used for this? Thank you Daniele -- ἀρετή --------------------------------------- Daniele de Sanctis, PhD Structural Biology Group ESRF, Grenoble, France Tel 33 (0)4 76 88 2869 ________________________________ 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=Gdo3XhHNq4Q8EvTyIOuKcGmWgGJNGSRAlBZTL7CGnCc&s=zf0W1v2hNpjNiCH51uuDnsPp1HJMSGwT3BVyEsh5Q-U&e=> -- Wim Burmeister Professeur Institut de Biologie Structurale (IBS) CIBB 71 avenue des Martyrs / CS 20192 38044 Grenoble Cedex 9, FRANCE E-mail: wim.burmeis...@ibs.fr<mailto:wim.burmeis...@ibs.fr> Tel: +33 (0) 457 42 87 41 Fax: +33 (0) 476 20 94 00 website<https://urldefense.proofpoint.com/v2/url?u=http-3A__www.ibs.fr_research_research-2Dgroups_viral-2Dreplication-2Dmachines-2Dgroup-2Dm-2Djamin_team-2D03_article_poxvirus-2Dreplication-2Dmachinery-2Dpresentation_&d=DwMFaQ&c=Dbf9zoswcQ-CRvvI7VX5j3HvibIuT3ZiarcKl5qtMPo&r=HK-CY_tL8CLLA93vdywyu3qI70R4H8oHzZyRHMQu1AQ&m=Gdo3XhHNq4Q8EvTyIOuKcGmWgGJNGSRAlBZTL7CGnCc&s=TVW6imEeLjhMO1RdtSLG3TllkHecM_5maLbcKjHXCz4&e=> map<https://urldefense.proofpoint.com/v2/url?u=https-3A__www.openstreetmap.org_-3Fmlat-3D45.20762-26mlon-3D5.69255-23map-3D17_45.20762_5.69255&d=DwMFaQ&c=Dbf9zoswcQ-CRvvI7VX5j3HvibIuT3ZiarcKl5qtMPo&r=HK-CY_tL8CLLA93vdywyu3qI70R4H8oHzZyRHMQu1AQ&m=Gdo3XhHNq4Q8EvTyIOuKcGmWgGJNGSRAlBZTL7CGnCc&s=33gxRvSYsfe6lNb5yCJtn24j5teEr8hJdd38jfs7M3k&e=> Changement climatique : «Les autres combats n’ont aucun sens si celui-là est perdu» (Aurélien Barrau) ________________________________ 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=Gdo3XhHNq4Q8EvTyIOuKcGmWgGJNGSRAlBZTL7CGnCc&s=zf0W1v2hNpjNiCH51uuDnsPp1HJMSGwT3BVyEsh5Q-U&e=> ######################################################################## To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB&A=1
