Hi Francis,
As you may have guessed - my question is stems from my recent
acquisition of some native data for a protein that I have lots of SAXS
data for.
I suspect that more conventional MR is unlikely to work in this case
as I only have a half-decent phasing model for ~30% of the protein (2
copies in the ASU, so 2x15%).
I figured that seeing as I had all this SAXS data (and I have many
datasets collected at multiple synchrotrons that all give very
consistent results), I might as well have a pop at phasing with it. I
have an Fsearch run running at the moment using Flms generated from
the Crysol program (ATSAS package) - no output as yet - does this
program only output results to the log file at the end of the run?
I have about 6 weeks until my next available synchrotron time, where
derivatives will be screened, better resolution native data will
hopefully be obtained, etc. In the meantime...
Cheers,
Dave
============================
David C. Briggs PhD
Father, Structural Biologist and Sceptic
============================
University of Manchester E-mail:
[log in to unmask]
============================
Webs : http://flavors.me/xtaldave
Twitter: @xtaldave
Skype: DocDCB
============================
On 12 March 2012 22:09, Francis E Reyes <[log in to unmask]> wrote:
> Hi David
>
> I'm the original poster you mention in your email, and I'm sad to report I never really got anywhere with the initial inquiry outside of James Holton's original response.
>
> The good news is that I was able to solve the structure I mentioned at 4A. (albeit through other means).
>
>
> From my own literature research I can vaguely remember that bridging the SAXS resolution to the X-ray resolution required measuring some really low angle reflections in the x-ray data (100-20A). And of course it's the phase extension piece that James refers to. (20A to 4A is a hell of a jump). However, even John Tainer has suggested that SAXS envelopes can be used to locate heavy atoms in isomorphous or anomalous difference data, though this has yet to be shown in practice. Depending on the heavy atom this can certainly help with the phase extension.
>
>
> Was your question academic, or are you, like I was, stuck in low resolution land with no phases? (I can certainly assist with the latter).
>
>
> F
>
>
>
>
>
>
> On Mar 12, 2012, at 2:10 PM, David Briggs wrote:
>
>> Hi CCP4bb,
>>
>> I would like to ask about "envelope phasing" - specifically with SAXS data.
>>
>> There are papers (1) and tutorials (2) describing how this might be
>> done, but I have also found comments on the ccp4bb, such as this one
>> (http://www.proteincrystallography.org/ccp4bb/message11690.html) which
>> are somewhat less optimistic.
>>
>> I get the impression from my reading around that SAXS envelope phasing
>> is somewhat difficult to do unless you have some NCS you can use to
>> help the phase extension process. Does anybody have any
>> opinions/evidence/examples/anecdotes/tips about how SAXS envelope
>> phasing can be done successfully?
>>
>> Cheers,
>>
>> Dave
>>
>> (1) - eg - http://scripts.iucr.org/cgi-bin/paper?dz5081
>> (2) - eg - http://www.phaser.cimr.cam.ac.uk/index.php/Using_Electron_Density_as_a_Model
>>
>> ============================
>> David C. Briggs PhD
>> Father, Structural Biologist and Sceptic
>> ============================
>> University of Manchester E-mail:
>> [log in to unmask]
>> ============================
>> Webs : http://flavors.me/xtaldave
>> Twitter: @xtaldave
>> Skype: DocDCB
>> ============================
>
>
>
> ---------------------------------------------
> Francis E. Reyes M.Sc.
> 215 UCB
> University of Colorado at Boulder
>
>
>
>
>
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