I'd advise A LOT of caution here. If you're new to the technique, there are several considerations to make well before you go docking a structure into a reconstruction. Some suggestions:
1. Is your sample truly singular? BSA is a wonderful example of this conundrum: at high enough concentrations, BSA can be seen sampling a monomer-dimer-trimer equilibrium. (seen as plain as day for BSA in SEC-MALS, SV, SE..) Did you scatter a monomer, or a mixture? SAXS profiles are a volume weighted averages of the scatter of the individual components, so those trimers and dimers, even in small amounts, are contaminating your signal and hence the data upon which your reconstructions are based (hence volumes are skewed). Is mass by I(0) or Qr that of a monomer? Is Rg concentration dependent? 2. Is your particle compact or flexible? Flexible species and lack of compactness undermine the reliability of a shape reconstruction. (see Kratky and Porod Debye Plots) 3. What is the chi for an individual reconstructions in your calculations? 4. What is the NSD (Normalized Spatial Discrepancy) for the 10++ individual calculations that you performed using DAMMIF/N or GASBOR? If that number is too high for what the program prescribes (also seen visually), are you then justified in averaging those shapes together? 5. Is your atomic inventory complete (vs the construct you scattered) - very difficult to reconcile these volumes with partial structures without landmarks or contrast variation. The missing bits matter. 6. Be sure your bead file is properly rendered in Pymol with the bead radius prescribed in the header of the damfilt file. Wrong bead sizes or just rendering a surface over the beads are very misleading in assessing the volume intended by the protein. What you show below does not look proper. Use the 'set sphere_scale, X.X' command to set the bead radius. If you pass those many criteria, then you're ready to dock a structure into a reconstruction. A good reality check before this would be to start with CRYSOL and see what the discrepancy between the structure and the primary scattering and in what part of the data those discrepancies lie. I can suggest a number of citations on each of the bullet points above if you'd like. Good Luck, Kushol Kushol Gupta, Ph.D. Research Associate - Van Duyne Group 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 Ritika Sethi Sent: Friday, June 26, 2015 5:42 AM To: CCP4BB@JISCMAIL.AC.UK Subject: Re: [ccp4bb] How to fit BioSAXS shape to the Structure I use SUPCOMB from the ATSAS package to fit the Xtal structure to the SAXS model. Then open this fitted file and your SAXS model again in pymol and you'll see the fit. From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Weifei Chen Sent: 26 June 2015 04:56 To: CCP4BB@JISCMAIL.AC.UK Subject: [ccp4bb] How to fit BioSAXS shape to the Structure Dear all, I am new to saxs and I get the model by saxs data and I have a structure. I want to fit the structure to the shape but I can just open them in PyMol. Can any one teach me to fit them? Best, Weifei
