Re: [ccp4bb] How to fit BioSAXS shape to the Structure

twinowski > 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 co

Re: [ccp4bb] How to fit BioSAXS shape to the Structure

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 A

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)

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, SAX

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

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 Profe

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 On 26 June 2015 at 11:39, Ashok Nayak wrote: > Dear Weifei, > > It can also be done manually in

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

Re: [ccp4bb] How to fit BioSAXS shape to the Structure

.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

Re: [ccp4bb] How to fit BioSAXS shape to the Structure

CP4BB@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:image00

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" 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, You might want to use SUPCOMB from the ATSAS suite. http://www.embl-hamburg.de/biosaxs/supcomb.html Cheers, Deborah.

[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