Dear Pascal, the EM2DAM program from the ATSAS package for SAXS (https://www.embl-hamburg.de/biosaxs/manuals/em2dam.html <https://www.embl-hamburg.de/biosaxs/manuals/em2dam.html>) can convert any EM envelope to a dummy-atom model in pdb format. Also, the recent SUPALM algorithm might provide additional options as well. http://journals.iucr.org/j/issues/2016/03/00/ap5002/ap5002.pdf <http://journals.iucr.org/j/issues/2016/03/00/ap5002/ap5002.pdf>
best wishes Savvas ---- Savvas Savvides Ghent University, L-ProBE VIB Inflammation Research Center (IRC) Technology Park 927, B-9052 Ghent (Zwijnaarde), Belgium +32 (0)472 928 519 (mobile) ; +32 9 331 36 60 (office) ; Skype: savvas.savvides_skype http://www.vib.be/en/research/scientists/Pages/Savvas-Savvides-Lab.aspx <http://www.vib.be/en/research/scientists/Pages/Savvas-Savvides-Lab.aspx> > On 25 Oct 2016, at 10:00, Randy Read <rj...@cam.ac.uk> wrote: > > Dear Pascal, > > I'm assuming that you're talking about using the negative stain image as an > MR model. I don't recall hearing of this having ever worked (though I would > be very interested of course if anyone has managed to do this!), but my > intuition is that it's not going to work. Negative stain just gives you an > external shape, whereas a cryo-EM reconstruction has internal features as > well. > > Presumably you don't have atomic models of the individual components of the > complex? If you did, using those directly for MR would be my first choice, > but you could also consider making a pseudo-atomic model by docking them into > the shape of the negative stain image. Such a model would add substantial > higher-resolution information. > > Best wishes and good luck, > > Randy Read > >> On 25 Oct 2016, at 02:49, Pascal Egea <pas...@msg.ucsf.edu >> <mailto:pas...@msg.ucsf.edu>> wrote: >> >> Dear All, >> >> I would like to know if it is possible to use a low resolution EM >> reconstruction of a complex obtained in negative stain EM (not cryo EM) to >> help molecular replacement in a 4.5A resolution X-ray diffraction data set >> of the same complex >> I am aware of the possibility of using low resolution cryoEM maps for MR as >> described in the review from Jackson et al in Nature Protocols but I was >> wondering if there is an intrinsically impossibility for negative stain >> reconstructions. >> >> Any thoughts or advice will be greatly appreciated. >> >> Best, >> >> -- >> Pascal F. Egea, PhD >> Assistant Professor >> UCLA, David Geffen School of Medicine >> Department of Biological Chemistry >> Boyer Hall room 356 >> 611 Charles E Young Drive East >> Los Angeles CA 90095 >> office (310)-983-3515 >> lab (310)-983-3516 >> email pegea at mednet.ucla.edu <http://mednet.ucla.edu/> > > ------ > 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: rj...@cam.ac.uk > <mailto:rj...@cam.ac.uk> > Cambridge CB2 0XY, U.K. www-structmed.cimr.cam.ac.uk > <http://www-structmed.cimr.cam.ac.uk/>
