I am no expert, but a) a very strong peak 7A from the origin means two molecules 7A apart?? Most unlikely ..
The first thing to look at is the actual images - Lattice translation defects usually generate very streaky patterns. Integration programs can cleverly select a lattice and ignore the unpredicted pixels - (by the way - why don't the data integration programs scream when this occurs? ) LTDs usually produce some strange intensity statistics too - what do the moments/twin tests etc look like? Otherwise your spacegroup must be wrong, although providing you have got the right crystalclass, I cant think how that can generate such a Patterson peak.. Good luck Eleanor PS - maybe search out another crystal! On Wed, 12 Feb 2020 at 10:25, Harry Powell - CCP4BB < 0000193323b1e616-dmarc-requ...@jiscmail.ac.uk> wrote: > Hi > > Something else I should have mentioned - in iMosflm you can sum your > images for viewing only if you have them as HDF5 or Pilatus CBF (as well > as summing them for processing if you have HDF5). > > Harry > > On 12 Feb 2020, at 10:18, Schreuder, Herman /DE < > herman.schreu...@sanofi.com> wrote: > > 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 > > > > 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 > 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 > > > > ------------------------------ > > To unsubscribe from the CCP4BB list, click the following link: > https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB&A=1 > ######################################################################## To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB&A=1
