My two cent suggestion: if you have a good atomic inventory, perform the fitting directly against the experimental profile using your partial structures in programs like CORAL and SASSIE and EOM; use the bead model as a corroborating result.
SAXS-derived ab initio bead models really aren’t the same thing as EM reconstructions, and can be horribly misleading if parts of your atomic inventory are flexible or disordered. (what are your NSD values for the bead calculations using what program? What do your Kratky and Porod-Debye plots look like?) Kushol Kushol Gupta, Ph.D. Research Assistant Professor Department of Biochemistry and Biophysics Perelman School of Medicine at The University of Pennsylvania <mailto:kgu...@upenn.edu> kgu...@upenn.edu / 215.573.7260 / 267.259.0082 / <http://www.stwing.upenn.edu/~kgupta> www.stwing.upenn.edu/~kgupta From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of dritan.siliqi Sent: Friday, November 4, 2016 4:51 PM To: CCP4BB@JISCMAIL.AC.UK Subject: [ccp4bb] R: [ccp4bb] fit multiple structures into SAXS envelope You can try with sculptor http://sculptor.biomachina.org In this pgm you can calculate first a map (a bĺured model) from saxs model (dammif) , then load your xray models and fit them simultaneously into the envelope. for the fitted model you can then calculate the saxs curve and compare with saxs data. D Dritan Siliqi Institute of Crystallography- CNR Via G. Amendola, 122/O 70126 Bari, Italy Phone: +39 0805929164 <tel:+39%200805929164> Fax: +39 0805929170 <tel:+39%200805929170> Email: dritan.sil...@ic.cnr.it skypeID: dritano Inviato da smartphone Samsung Galaxy. -------- Messaggio originale -------- Da: Natalia O <natalie.c...@gmail.com> Data: 04/11/16 21:32 (GMT+01:00) A: CCP4BB@JISCMAIL.AC.UK Oggetto: [ccp4bb] fit multiple structures into SAXS envelope Dear All, I have a question regarding SAXS, I collected SAXS data on the protein of interest and I can generate the molecular envelope, I also solved x-ray structures of its domains, and I would like to fit my x-ray structures into SAXS envelope, or alternatively find some program which could assemble my domains based on the original SAXS data (not even based on the processing product -envelope). I know that CRYSOL can produce a scattering curve based on some given X-ray structures, but to use it, I would have to fit my x-ray structures in the envelope manually, and then produce the scattering curve to compare with the experimental curve. However, I wonder if there is a program that could do the fitting itself? Thank you! Yours, Natalia
