Re: [ccp4bb] How to fit BioSAXS shape to the Structure
Dear Weifei, You might want to use SUPCOMB from the ATSAS suite. http://www.embl-hamburg.de/biosaxs/supcomb.html Cheers, Deborah.
Re: [ccp4bb] How to fit BioSAXS shape to the Structure
SITUS is another good option. R From my iPhone On 26 Jun 2015, at 08:20, Deborah Harrus har...@free.fr wrote: Dear Weifei, You might want to use SUPCOMB from the ATSAS suite. http://www.embl-hamburg.de/biosaxs/supcomb.html Cheers, Deborah.
Re: [ccp4bb] How to fit BioSAXS shape to the Structure
Dear Weifei, in my experience you can try a couple of things: * Use SUPCOMB which is a part of the ATSAS package * Use SITUS to fit your structure into the envelope (SITUS can be downloaded here: http://situs.biomachina.org and also contains a tutorial specifically for this type of application) * Use SITUS to generate an envelope based on your DAM (dummy atom model) and fit the structure into the envelope using the fitting function within UCSF Chimera. Hope this helps, Yann ir. Yann Sterckx, PhD Post-doc Stefan Magez lab Structural Biology Research Center (SBRC: http://sbrc.vub.ac.be) Vrije Universitetit Brussel (VUB) Vlaams Instituut Biotechnologie (VIB) VUB - SBRC Building E, 8th floor Pleinlaan 2 B-1050 Brussels Belgium +32-02-629 19 77 e-mail: yann.ster...@vib-vub.be or sterckx.y...@gmail.com On 26 Jun 2015, at 05:56, Weifei Chen weife...@outlook.com wrote: 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 ghfijice.png
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
Re: [ccp4bb] How to fit BioSAXS shape to the Structure
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
Re: [ccp4bb] How to fit BioSAXS shape to the Structure
Shouldn't the ability to distinguish enantiomers also depend upon the degree of asymmetry of the particle itself? (or pseudosymmetry, I suppose) With SAXS it should be easier to distinguish right-handed and left-handed lock washers than it is to tell a right-handed from a left-handed wall screw. On Fri, Jun 26, 2015 at 2:14 PM, Reza Khayat rkha...@ccny.cuny.edu wrote: 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
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 [cid:image001.png@01D0AFFC.C020F870]
Re: [ccp4bb] How to fit BioSAXS shape to the Structure
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
Re: [ccp4bb] How to fit BioSAXS shape to the Structure
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
Re: [ccp4bb] How to fit BioSAXS shape to the Structure
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
Re: [ccp4bb] How to fit BioSAXS shape to the Structure
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.orghttp://www.khayatlab.org On Jun 26, 2015, at 6:50 AM, David Briggs drdavidcbri...@gmail.commailto:drdavidcbri...@gmail.com wrote: SASTBX has an online tool for achieving this: http://sastbx.als.lbl.gov/cgi-bin/superpose.html http://about.me/david_briggs [David Briggs on about.me] David Briggs about.me/david_briggs On 26 June 2015 at 11:39, Ashok Nayak ashokgocrac...@gmail.commailto: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
Re: [ccp4bb] How to fit BioSAXS shape to the Structure
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
