Thanks Eleanor, I tried MR for P32 21 and P32 12.
SG P3221: SOLU SET RFZ=5.3 TFZ=8.8 PAK=0 LLG=121 TFZ==11.2 LLG=944
TFZ==29.2 PAK=0 LLG=944 TFZ==29.2
SOLU SPAC P 32 2 1
SG P3212:
Solution #1 annotation (history):
SOLU SET RFZ=4.4 TFZ=7.7 PAK=0 LLG=55 TFZ==9.6 LLG=350 TFZ==20.5
PAK=0 LLG=350 TFZ==20.5
SOLU SPAC P 32 1 2
SG P32
SOLU SET RFZ=7.4 TFZ=10.4 PAK=0 LLG=187 TFZ==10.7 RF++ TFZ=17.0 PAK=0
LLG=436 TFZ==17.8 LLG=1715 TFZ==34.3 PAK=0
LLG=1715 TFZ==34.3
SOLU SPAC P 32
Based on TFZ and LLG, the P32 seems to be best. But I'll also try to
refine and build P32 2 1 latter
On Fri, Apr 14, 2017 at 4:32 AM, Eleanor Dodson <eleanor.dod...@york.ac.uk>
wrote:
> First - four way twinning is possible but pretty rare for macromolecules
>
> Pointless gives a very useful table of the CC agreement for each possible
> symmetry operator individually.
> In this case with only two molecules in the asymmetric unit you you could
> only have a higher symmetry SG as
> P32 21 P32 12 or P64
>
> These would require as symmetry operators -
> P32 21 - a three fold and a two fold k h -l
> P32 12 - a three fold and a two fold -k -h -l
>
> P64 - a six fold
>
> If the scores for one set are better than the others you probably have
> that SG
>
> However high degrees of twinning can disguise the symmetry scores of
> course..
>
>
>
> On 14 April 2017 at 04:46, Keller, Jacob <kell...@janelia.hhmi.org> wrote:
>
>> Try MR with one copy in all space groups of PG 321/312 using Phaser.
>> Going from PG 3 to PG 32 should halve the number of copies per ASU. You may
>> have to re-process your data in the higher point group to do this.
>>
>>
>>
>> Or you might actually have a tetartohedral twin, but just try with the
>> higher-symmetry point group first, see what happens.
>>
>>
>>
>> JPK
>>
>>
>>
>> *From:* Alex Lee [mailto:alexlee198...@gmail.com]
>> *Sent:* Thursday, April 13, 2017 11:32 PM
>>
>> *To:* Keller, Jacob <kell...@janelia.hhmi.org>
>> *Cc:* CCP4BB@JISCMAIL.AC.UK
>> *Subject:* Re: [ccp4bb] Refmac5 twin refinement pushing Rfree
>> surprisingly down
>>
>>
>>
>> Hi Keller,
>>
>>
>>
>> Thanks for the suggestions! I only have two copies in ASU at SG P32.
>> Zanuda also suggests P32 is the best SG.
>>
>>
>>
>> On Thu, Apr 13, 2017 at 8:12 PM, Keller, Jacob <kell...@janelia.hhmi.org>
>> wrote:
>>
>> Yes, this was my case exactly—it looks like there are two pairs of
>> coupled twin domains: a,c and b,d. Assuming you have multiple copies of
>> your model in the same ASU, try doing MR in higher symmetry space groups of
>> point group 312 or 321, like P3212 etc. There is this handy page with all
>> the space groups and their possible twin operators:
>> http://www.ccp4.ac.uk/html/twinning.html.
>>
>>
>>
>> The twin fractions indicate a high twin fraction—~46% if actually
>> hemihedral!
>>
>>
>>
>> Also take a look at the paper I referenced for more info. I can send you
>> a .pdf if you need me to.
>>
>>
>>
>> Please let me know how it works out—I am interested in these types of
>> things!
>>
>>
>>
>> JPK
>>
>>
>>
>> *From:* Alex Lee [mailto:alexlee198...@gmail.com]
>> *Sent:* Thursday, April 13, 2017 9:08 PM
>> *To:* Keller, Jacob <kell...@janelia.hhmi.org>
>> *Cc:* CCP4BB@JISCMAIL.AC.UK
>>
>>
>> *Subject:* Re: [ccp4bb] Refmac5 twin refinement pushing Rfree
>> surprisingly down
>>
>>
>>
>> Hi Keller,
>>
>>
>>
>> I do not how to check twin fraction after Refmac (I guess it's somewhere
>> in log file). From the log file it seems I have four twin domain:
>>
>> Twin operators with estimated twin fractions ****
>>
>>
>>
>> Twin operator: H, K, L: Fraction = 0.275; Equivalent operators: K, -H-K,
>> L; -H-K, H, L
>>
>> Twin operator: -K, -H, -L: Fraction = 0.228; Equivalent operators: -H, H+K,
>> -L; H+K, -K, -L
>>
>> Twin operator: K, H, -L: Fraction = 0.270; Equivalent operators: H, -H-K,
>> -L; -H-K, K, -L
>>
>> Twin operator: -H, -K, L: Fraction = 0.228; Equivalent operators: -K, H+K,
>> L; H+K, -H, L
>>
>>
>>
>> On Thu, Apr 13, 2017 at 4:36 PM, Keller, Jacob <kell...@janelia.hhmi.org>
>> wrote:
>>
>> What was the refined twin fraction after Refmac? It’s much more accurate
>> than initial tests. Also, how many twin domains do you have? If you have
>> many, it might be a higher space group but with less twinning. I recently
>> had a case in which apparent tetartohedral (four-domain) twinning in P32
>> was really hemihedral (two-domain) twinning in P3212:
>>
>>
>>
>> *Acta Cryst. <http://journals.iucr.org/d>* (2017). D*73*
>> <http://journals.iucr.org/d/contents/backissues.html>, 22-31
>> https://doi.org/10.1107/S2059798316019318
>>
>>
>>
>> Jacob
>>
>>
>>
>> *From:* CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] *On Behalf Of
>> *Eleanor Dodson
>> *Sent:* Thursday, April 13, 2017 3:11 PM
>> *To:* CCP4BB@JISCMAIL.AC.UK
>> *Subject:* Re: [ccp4bb] Refmac5 twin refinement pushing Rfree
>> surprisingly down
>>
>>
>>
>> Twin refinement cannot be compared directly to untwinned - the R factors
>> are between different parameters - without twinning it is assumed you have
>> an amplitude obtained more or less from sqrt(I But for a twinned data set
>> that I is actually [ I1 + twin_factor I2 ] so the amplitude is not really
>> correct and twinned refinement will give a much better estimate.
>>
>>
>>
>> However you need to be careful that you have assigned the same FreeR flag
>> to reflection pair related by the twin law. The modern program in the CCP4
>> data reduction pipeline looks after this pretty automatically - all
>> possible symmetry equivalents are assigned the same FreeR but older
>> software did not do this..
>>
>>
>>
>> You can check it by looking at some twin equivalents - in SG P32 these
>> could be h k l and -h, -k, l or h k l and k h -l or h k l and -k, -h, -l .
>>
>>
>>
>> Ideally they all should have the same Free R flag..
>>
>>
>>
>> Eleanor
>>
>>
>>
>> PS - the acid test is: Do the maps look better?
>>
>>
>>
>> E
>>
>>
>>
>>
>>
>> On 13 April 2017 at 19:52, Robbie Joosten <r.joos...@nki.nl> wrote:
>>
>> Hi Alex,
>>
>>
>>
>> You are not giving the number after refinement without the twin
>> refinement. Nevertheless, R-free drops like this are not unheard of. You
>> should check your Refmac log file, it would warn you of potential space
>> group errors. Refmac will also give you a refined estimate of the twin
>> fraction.
>>
>>
>>
>> Cheers,
>>
>> Robbie
>>
>>
>>
>> Sent from my Windows 10 phone
>>
>>
>>
>> *Van: *Alex Lee <alexlee198...@gmail.com>
>> *Verzonden: *donderdag 13 april 2017 19:19
>> *Aan: *CCP4BB@JISCMAIL.AC.UK
>> *Onderwerp: *[ccp4bb] Refmac5 twin refinement pushing Rfree surprisingly
>> down
>>
>>
>>
>> Dear All,
>>
>>
>>
>> I have a protein/dna complex crystal and data collected at 3A and another
>> set at 2.8A, space group P32. L test shows twinning (fraction around 0.11).
>> The structure solved by MR and model building of the complex finish (no
>> solvent built yet, I do not think it's good to build solvent in such low
>> resolution data).
>>
>>
>>
>> I did Refmac5 to refine my structure (restraint refinement) with or
>> without twinning, to my surprise, the Rfree drops a lot after twin
>> refinement of two data sets. Summary below:
>>
>>
>>
>> 2.8A dataset: before twin refine 34%, 29%; after twin refine:24%, 19%
>>
>> 3A dataset: before twin refine 30%;26%; after refine 25%, 18%
>>
>>
>>
>> I know that a lot of threads in CCP4bb talking about Rfree after twin
>> refine and Rfree without twin refine can not compare directly. By drop R
>> free this much by twin refine, it gives me a feeling of too good to be true
>> (at such low resolution with such good Rfree, maybe overrefined a lot?),
>> but from the density map after twin refine, it does seem better than no
>> twin refine map.
>>
>>
>>
>> I do not know if reviewers are going to challenge this part.
>>
>>
>>
>> Any input is appreciated.
>>
>>
>>
>>
>>
>>
>>
>>
>>
>>
>>
>>
>>
>
>
