Re: [ccp4bb] [off topic] Fitting unknown model in SAXS envelope
Dear Andre, In the past I had some good fitting results with SITUS (it was a case where the matched the crystal structure). Best, D From: CCP4 bulletin board [CCP4BB@JISCMAIL.AC.UK] on behalf of Adam Round [aro...@embl.fr] Sent: 02 February 2015 11:13 To: ccp4bb Subject: Re: [ccp4bb] [off topic] Fitting unknown model in SAXS envelope 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.itmailto:dritan.sil...@ic.cnr.it skypeID: dritano -- This e-mail and any attachments may contain confidential, copyright and or privileged material, and are for the use of the intended addressee only. If you are not the intended addressee or an authorised recipient of the addressee please notify us of receipt by returning the e-mail and do not use, copy, retain, distribute or disclose the information in or attached to the e-mail. Any opinions expressed within this e-mail are those of the individual and not necessarily of Diamond Light Source Ltd. Diamond Light Source Ltd. cannot guarantee that this e-mail or any attachments are free from viruses and we cannot accept liability for any damage which you may sustain as a result of software viruses which may be transmitted in or with the message. Diamond Light Source Limited (company no. 4375679). Registered in England and Wales with its registered office at Diamond House, Harwell Science and Innovation Campus, Didcot, Oxfordshire, OX11 0DE, United Kingdom
[ccp4bb] [off topic] Fitting unknown model in SAXS envelope
Dear usersI'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
Re: [ccp4bb] [off topic] Fitting unknown model in SAXS envelope
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
Re: [ccp4bb] [off topic] Fitting unknown model in SAXS envelope
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
Re: [ccp4bb] [off topic] Fitting unknown model in SAXS envelope
Andre, some suggestions: 1. First be sure that shape reconstructions as an approach to interpreting your data is justified – the shape reconstruction approach can be quite misleading in some circumstances: i. Does your data show any evidence of flexibility and lack of compactness from Kratky and Porod-Debye analyses? Such aspects can exaggerate molecular volumes, undermining the ability to implement shape reconstruction algorithms to arrive at stable solutions. Extra floppy bits like extended linkers his-tags and mixtures of conformations can also affect apparent volumes. ii. Does your data agree with your understanding of molecular mass at those concentrations (e.g., Mass by Qr, Mass by I(0), Mass by empirical relationships with Porod Volume, etc.). Does Oligomer/Mixture analysis tell you that you have all tetramer, rather than say 95% tetramer/5% dimer…? Is there evidence of aggregation or concentration-dependence through multiple concentrations? As one can guess, mixtures and aggregation can undermine reliable shape reconstruction and interpretation. iii. How does the atomic inventory of your model compare to that of the reconstruction? Commonly, x-ray crystal structures are missing sequences that might otherwise be in a full-length/native construct. If your scattered sample has a composition not entirely represented in your atomic model, automated approaches might be misled, and doing it by eye might be difficult without obvious landmarks or constraints. It could be very helpful to scatter a few different truncations and then to employ simultaneous solution approach used in MONSA. Increasing your data-to-parameters always helps! iv. How does a CRYSOL/FOXS fit between your model and the primary data look, independent of the shape reconstruction calculations? v. Does a symmetry-free (P1) calculation using DAMMIF or GASBOR agree with a symmetry-imposed calculation?...What is the distribution of the Normalized Spatial Discrepancies (NSDs) and Chis like for 10+ calculations? Is averaging justified by the statistics? 2. With regards to software suggestions, in addition to SUPCOMB, I might suggest looking at the SITUS/SCULPTOR package. It uses a real-space approach to reconcile atomic models with volumetric representations, and does provide a real-space correlation coefficient for fits. Hope that helps, 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 Andre Godoy Sent: Monday, February 2, 2015 5:53 AM To: CCP4BB@JISCMAIL.AC.UK Subject: [ccp4bb] [off topic] Fitting unknown model in SAXS envelope 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
Re: [ccp4bb] [off topic] Fitting unknown model in SAXS envelope
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
