[phenixbb] twin/pseudo-symmetry question

[Peter Zwart]

yes,

you should be able to use the obverse/reverse twin law when you refine
in the hexagonal setting.

Do the intensity statistics indicate that data is twinned though?

Your C2 refinement with its low r value can be due to bias if the free
set hasnt been chosen carefully.


P

On 11 November 2011 11:05, Green, Todd <green at cbse.uab.edu> wrote:
> Regarding imosflm and full control, I remember reading about the variant choices for C2 somewhere. So somewhere I have the files from imosflm done this way. I just never went beyond the processing to see what happens. So there is room to check.
>
> I'll also check for the integral absences to check for the obverse/reverse twin. If this is the case. Can I apply an twin operation to the refinement? I'll spend some time googling this.
>
> Thanks also for the info regarding rfree selection (including you Nat) I can just reverse course and import the original scalepack file (or imosflm files rather) and follow the refinement as i just did.
>
> If the current refinement in C2 (with twin) were correct, are the numbers r_work = 0.1582 r_free = 0.1866 too low to be reasonable?
>
> Thanks -
> Todd
>
>
> -----Original Message-----
> From: phenixbb-bounces at phenix-online.org on behalf of Peter Zwart
> Sent: Fri 11/11/2011 12:28 PM
> To: PHENIX user mailing list
> Subject: Re: [phenixbb] twin/pseudo-symmetry question
>
> Hi Todd,
>
> There are 3 possible C2's you can choose from. Try besides R32
>
> R3
> C2 (no 1)
> C2 (no 2)
> C2 (no 3)
> P1
>
> If you use labelit / imosflm you have full control over which
> spacegroup you can choose. HKL2000 doesn't provide enough control over
> which indexing solution you want to use.
>
> Alternatively, you could have an 'obverse/reverse twin' in R32, a
> special kind of reticular twin. In this twinning form, the hexagonal
> sublattice causes the twinning. When you index your data, check if the
> integral absences are indeed absent (when you are in the hexagonal
> setting). If not, you could have an obverse reverse twin.
>
> I have no clue about CCP4, but in phenix selecting the free set is
> done properly using the full symmetry of the lattice. If this is done
> incorrectly, you will get in trouble later down the line, so better
> make sure that things are ok.
>
> P
>
>
>
>
> On 11 November 2011 10:03, Green, Todd <green at cbse.uab.edu> wrote:
>> For the R32 set, I generate the r-free in phenix directly from the scalepack file for data processed in R32. For C2, it was generated from the C2 processed scalepack file but in ccp4 using the scalepack2mtz script then imported to phenix(because i used molrep for the molecular replacement). But, I kept this same data file with the same r-free for all of the refinement runs before and during twin refinement. Seem reasonable?
>>
>> -Todd
>>
>>
>> -----Original Message-----
>> From: phenixbb-bounces at phenix-online.org on behalf of Nathaniel Echols
>> Sent: Fri 11/11/2011 11:53 AM
>> To: PHENIX user mailing list
>> Subject: Re: [phenixbb] twin/pseudo-symmetry question
>>
>> On Fri, Nov 11, 2011 at 9:47 AM, Green, Todd <green at cbse.uab.edu> wrote:
>>> the true space group is C2. Are these r-values too low? does the difference
>>> in values according to each twin law mean something?
>>
>> I don't know enough to answer the rest of the question, but one thing
>> to look out for is how you generate the R-free flags - which program
>> did you use, and when you reprocessed in C2, did you generate a new
>> set of R-free flags?  If you're not careful with this, you can end up
>> severely biasing R-free when performing twinned refinement.
>>
>> -Nat
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>>
>
>
>
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> -----------------------------------------------------------------
> P.H. Zwart
> Research Scientist
> Berkeley Center for Structural Biology
> Lawrence Berkeley National Laboratories
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-- 
-----------------------------------------------------------------
P.H. Zwart
Research Scientist
Berkeley Center for Structural Biology
Lawrence Berkeley National Laboratories
1 Cyclotron Road, Berkeley, CA-94703, USA
Cell: 510 289 9246
BCSB:      http://bcsb.als.lbl.gov
PHENIX:   http://www.phenix-online.org
SASTBX:  http://sastbx.als.lbl.gov
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