Dear Eleanor,
I have used the ACORN previously for structure solution but I will have to
read more about its functionality in structure refinement.
I have run two Refmac jobs using either native or anomalous data with
otherwise default parameters resulting in R/Rfree of 0.2013/0.2458 and
0.1862/0.2274 respectively for crystal diffracting to ~1.85A. This seems to
me, that using anomalous signal in refinement can be useful at least in
some cases.
Regards,
Piotrek
Hmm - you can certainly generate "MAD" phases using the anom signal from
one data set, and then PARROT or some such density modification tool to
extend those phases for the higher resolution reflections..
Or ACORN can work well if he data resolution is high enough to give good
phases for all the data
Then you can use those phases in the initial refinement procedure - the
usual idea is to use them till the R factor drops below 30% or 35% then
just refine against the Fobs, phasing just from the model .
But I dont think it is ever worth working at a limited resolution..
Dear Eleanor,
thank you for your comment. My crystals of interest diffract with dmin
usually between 1.4 and 1.9 A (in high energy data set) and significant
anomalous signal extends usually to approx. 4 A (in low energy data set).
Certainly I do agree, that in "EITHER, OR" situation one can check both
approaches, compare the results and take the more convincing one. I can
easily do that in Refmac running one job against data with Friedel pairs
merged and parallel one against data with Friedel pairs unmerged. I was
considering rather an "AND" scenario in which in addition to high
resolution data (FP) I'd include information from anomalous signal (F+ F-,
DANO). I understand that this should increase number of observations from a
given sample and therefore help to refine positions, occupancies and
perhaps ADPs for at least a fraction of atoms in a model (Mn ions and S in
my case). I imagine it as somehow analogical to adding geometrical
restrains derived from very high resolution data to refinement protocols.
I was wondering first of all if my reasoning is sensible and if there is an
existing protocol to try this?
With kind regards,
Piotrek
czw., 3 sty 2019 o 22:00 Eleanor Dodson <[email protected]>
napisał(a):
> Hmm - you can certainly generate "MAD" phases using the anom signal from
> one data set, and then PARROT or some such density modification tool to
> extend those phases for the higher resolution reflections..
> Or ACORN can work well if he data resolution is high enough to give good
> phases for all the data
>
>
> Then you can use those phases in the initial refinement procedure - the
> usual idea is to use them till the R factor drops below 30% or 35% then
> just refine against the Fobs, phasing just from the model .
>
> But I dont think it is ever worth working at a limited resolution..
>
> eleanor
>
> On Thu, 3 Jan 2019 at 20:40, Piotr Wilk <[email protected]> wrote:
>
>> Dear Eleanor,
>>
>> thank you for your comment. My crystals of interest diffract with dmin
>> usually between 1.4 and 1.9 A (in high energy data set) and significant
>> anomalous signal extends usually to approx. 4 A (in low energy data set).
>> Certainly I do agree, that in "EITHER, OR" situation one can check both
>> approaches, compare the results and take the more convincing one. I can
>> easily do that in Refmac running one job against data with Friedel pairs
>> merged and parallel one against data with Friedel pairs unmerged. I was
>> considering rather an "AND" scenario in which in addition to high
>> resolution data (FP) I'd include information from anomalous signal (F+ F-,
>> DANO). I understand that this should increase number of observations from a
>> given sample and therefore help to refine positions, occupancies and
>> perhaps ADPs for at least a fraction of atoms in a model (Mn ions and S in
>> my case). I imagine it as somehow analogical to adding geometrical
>> restrains derived from very high resolution data to refinement protocols.
>> I was wondering first of all if my reasoning is sensible and if there is
>> an existing protocol to try this?
>>
>> With kind regards,
>> Piotrek
>>
>> czw., 3 sty 2019 o 17:02 Eleanor Dodson <[email protected]>
>> napisał(a):
>>
>>> I think any decision depends on the resolution of your two data sets. If
>>> they are very different I would choose the higher resolution one.
>>>
>>> If that is the Anom data then I would use the anom signal at least in
>>> the first cycles to improve the phases..
>>>
>>> Eleanor
>>>
>>> On Thu, 3 Jan 2019 at 14:59, Piotr Wilk <[email protected]> wrote:
>>>
>>>> Dear CCP4 experts,
>>>>
>>>> I'd like to ask your opinion about using anomalous signal in refinement
>>>> of crystal structures in addition to using high resolution native data.
>>>> I am working on a series of structures for which I have collected two
>>>> data sets (from the same crystal):
>>>> 1 - native with higher resolution
>>>> 2 - anomalous at MN absorption edge peak.
>>>> The structures were solved with MR and preliminary refinement using the
>>>> native data only yields decent statistics, but I also use anomalous data to
>>>> verify presence and position of manganese ions. For this I used ANODE which
>>>> lists four strong peaks (~30 sigma) as expected for manganese ions and
>>>> around 45 weaker peaks (~9-5 sigma) for sulfur atoms in Cys and Met. I am
>>>> happy to use this information in model building but I was also wondering if
>>>> (and how) beneficial would it be to use both high resolution structure
>>>> factors and somehow lower resolution yet highly specific anomalous signal
>>>> in the same round of refinement?
>>>> In Refmac5 I can use either refinement with "no prior phase
>>>> information" taking FP and SIGFP or "SAD data directly" with SIGFP F(+)
>>>> SIGF(+) F(-) SIGF(-), but I didn't find any "MAD" option to use both.
>>>> I have the following columns in my mtz files:
>>>> for native data: H K L FP SIGFP FreeRflag
>>>> for anomalous data : H K L FP SIGFP F(+) SIGF(+) F(-) SIGF(-) FreeRflag
>>>> or : H K L FP SIGFP DANO SIGDANO ISYM
>>>> FreeRflag
>>>>
>>>> I could use CAD to merge the interesting columns into a single mtz file
>>>> containing:
>>>> H K L FP SIGFP FreeRflag F(+) SIGF(+) F(-) SIGF(-) DANO SIGDANO
>>>>
>>>> I'd appreciate any comments or advise how to use both sources of
>>>> information in the refinement.
>>>>
>>>> I wish you all a Happy New Year.
>>>> Kind regards,
>>>> Piotrek
>>>>
>>>>
>>>>
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