That's interesting. Enantiomer differences can be detected at worse than 20Angstrom resolution in EM reconstructions. What do you think is the reason for this?
Reza Khayat, PhD Assistant Professor Department of Chemistry City College of New York 85 Saint Nicholas Terrace, CDI 12318 New York, NY 10031 http://www.khayatlab.org/ 212-650-6070 -----Original Message----- From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Zbyszek Otwinowski Sent: Friday, June 26, 2015 11:43 AM To: CCP4BB@JISCMAIL.AC.UK Subject: Re: [ccp4bb] How to fit BioSAXS shape to the Structure At low resolution, without interpretable anomalous signal, neither SAXS nor molecular replacement with SAXS model, can distinguish correct from inverted solution. So inverted model will fit crystal data equally well. Only phase extension to much higher resolution (e.g. 5A) can help. > Yes, SAXS has an enantiomer problem - mirror image DAMMIN/F > reconstructions will give the same fit to the raw scattering data, > whereas your protein structure will only fit one hand. > > SUPCOMB can certainly deal with this problem, as detailed in > http://www.embl-hamburg.de/biosaxs/manuals/supcomb.html > > > > > [image: David Briggs on about.me] > > David Briggs > about.me/david_briggs > <http://about.me/david_briggs> > > On 26 June 2015 at 12:04, Reza Khayat <rkha...@ccny.cuny.edu> wrote: > >> Hi, >> >> Follow up question on SAXS. Does SAXS have an enantiomer problem >> like electron microscopy? In other words, does the calculated model >> possess the correct handedness or can both handedness of a model fit >> the scattering profile just as well? >> >> Best wishes, >> Reza >> >> Reza Khayat, PhD >> Assistant Professor >> City College of New York >> 85 St. Nicholas Terrace CDI 12308 >> New York, NY 10031 >> (212) 650-6070 >> www.khayatlab.org >> >> On Jun 26, 2015, at 6:50 AM, David Briggs <drdavidcbri...@gmail.com> >> wrote: >> >> SASTBX has an online tool for achieving this: >> http://sastbx.als.lbl.gov/cgi-bin/superpose.html >> >> >> >> [image: David Briggs on about.me] >> >> David Briggs >> about.me/david_briggs >> <http://about.me/david_briggs> >> >> On 26 June 2015 at 11:39, Ashok Nayak <ashokgocrac...@gmail.com> wrote: >> >>> Dear Weifei, >>> >>> It can also be done manually in Pymol by changing the mouse mode >>> from >>> 3 >>> button viewing to 3 button editing and later moving the envelope >>> onto the X-ray structure or vice-versa, however the best fit can be >>> achieved in SUPCOMB. >>> >>> regards >>> Ashok Nayak >>> CSIR-CDRI, Lucknow >>> India >>> >>> >> >> > Zbyszek Otwinowski UT Southwestern Medical Center at Dallas 5323 Harry Hines Blvd. Dallas, TX 75390-8816 Tel. 214-645-6385 Fax. 214-645-6353
