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