Andre, I agree with Adam. Rigid body modelling with the crystal structure or homology models using CORAL is the best way to proceed. Remember to model all of your molecule, even the missing bits. CORAL will use a chain of beads for missing N- and C- termini or short linkers. For missing domains the only option is to use an homology model, and remember that you are fitting the shape and not the secondary structure which, is beyond the resolution of your SAXS data.
An additional comment on the use of the probable molecular shape models generated by DAMMIN/DAMMIF. The term "envelope" is most misleading, as most people think of the CryoEM envelopes which are much more closely related to the actual experimental observations. The a priori bead models generated by these programs are encoded with user biases of their own. Did you use P1 or P2 symmetry for instance. The programs have options to generate --prolate or --oblate shapes, the default bias is --globular. If you choose the wrong one, your shape may be very biased, and not at all related to your actual molecular envelope. The biggest caveat with any SAXS model, is the quality of your data and sample. The smallest fraction of contaminant can make all of these analyses moot. -- Yours sincerely, Mark A. White, Ph.D. Associate Professor of Biochemistry and Molecular Biology, Manager, Sealy Center for Structural Biology and Molecular Biophysics Macromolecular X-ray Laboratory, Basic Science Building, Room 6.630 University of Texas Medical Branch Galveston, TX 77555-0647 Tel. (409) 747-4747 Cell. (281) 734-3614 Fax. (409) 747-1404 mailto://mawh...@utmb.edu http://xray.utmb.edu QQ: "If you look for truth, you may find comfort in the end; if you look for comfort you will not get either comfort or truth only soft soap and wishful thinking to begin, and in the end, despair." - C. S. Lewis -----Original Message----- From: Adam Round <aro...@embl.fr> Reply-to: Adam Round <aro...@embl.fr> To: CCP4BB@JISCMAIL.AC.UK Subject: Re: [ccp4bb] [off topic] Fitting unknown model in SAXS envelope Date: Mon, 2 Feb 2015 12:13:46 +0100 SUPCOMB will only give useful results if the shape of the SAXS envelope matches that in the Crystal structure. In this case with multiple subunits, fitting the chosen numbers of monomers to the SAXS data with SASREF (also from the ATSAS package) would be more appropriate. the resulting model should then be overlayed with the envelope using SUPCOMB for verification. Additional help on this can be found in the SAXIER forum: http://www.saxier.org/forum/ If you are interested in learning more regarding the complimentary use of SAS and MX you should consider attending a course such as the upcumming EMBO course in Grenoble (Deadline march 1st): http://events.embo.org/15-saxs/ Best regards Adam Round On 02/02/15 12:01, Dritan Siliqi wrote: > > I supposed could be done by supcomb program at ATSAS package > > -- > > On 02/02/2015 11:52, Andre Godoy wrote: > > > Dear users > > I'm having some troubles to fit my x-ray model in my SAXS envelope.. > > more about: > > > > > > 1) I have a SAXS model with enough room for 6 monomers. > > > > > > 2) I have the crystallographic structure, but AU or any generate > > symmetry related doesn't appears to be the biological unit (I mean, > > crystal packing is different from SAXS packing) > > > > > > Is there any piece of software that can take monomers and find the > > best (or least worst) RMSD between a SAXS envelope and a generated > > coordinate system? Or anyone have a good ideia for me to do so? > > > > > > All the best, > > > > > > Andre Godoy > > PhD Student > > IFSC - University of Sao Paulo - Brazil > > > > -- > Dritan Siliqi > Institute of Crystallography- CNR > Via G. Amendola, 122/O 70126 Bari, Italy > Phone: +39 0805929164 Fax: +39 0805929170 > Email: dritan.sil...@ic.cnr.it > skypeID: dritano
