On 2 Mar 2012, at 08:01, arka chakraborty wrote:

Hi all,

I will like to know, as a follow up of what Prof. Randy Read said, what should be done to do the refinement against the measured data and not the detwinned F( which refmac outputs in the mtz after twin refinement), during subsequent refinements.

Operationally, don't put in the "MTZ in" field of the GUI something that Refmac generated for you in a previous run as "MTZ out" file. Always use as "MTZ in" your original data file.

And also, I would like to know how to ensure that the free R generated takes twinning into account if I am not using phenix.

Refmac does take in consideration the twin law(s) when handling free reflections . This is the case even if you have generated your free reflections randomly. Internally Refmac will modify your Free set in such a way that twin related reflections are in the same group (free or working) --> classes mentioned by Garib

The good thing about this is that twin-related reflections are handled properly during refinement irrespective of your Free-set choice.

The bad thing (Garib please correct me if I am wrong here) is that you might end up depositing a Free set which is not that actually used in refinement.

Best wishes

Roberto

Thanks in advance,

Regards,

ARKO

On Fri, Mar 2, 2012 at 12:44 PM, Randy J. Read <[log in to unmask]> wrote:

I'm worried when you say that you use the initial job's output MTZ. Refmac replaces F with a detwinned F in the output file so you wouldn't be refining against your measured data in the subsequent round.

Best wishes

Randy Read

----
Randy J. Read

On 2 Mar 2012, at 02:00, wtempel <[log in to unmask]> wrote:

> Dear CCp4ers,
> A good morning to everyone.
> Today, I have a structure that I initially refined in space group P6522, 1mol/asu.
> Scaling stats (scalepack): 2.30-2.26A: Rsym=99.9%; <I>/<sigma> > 3
> 2.61-2.55A: Rsym=39.6%, <I>/<sigma> > 10
> 50.00-6.13: Rsym=6.4%
> Some mild anisotropy in the resolution limits is apparent on the diffraction images. Say, visible spots at 2.2A in one direction, 2.6A in the other.
> Rfree, using data to 2.3A, was stuck in mid-30%s. The map appears like 3.5A resolution, with some difference density for loops that cannot be interpreted with reasonable geometry.
> Rsym is very similar for data scaled in P3, in all resolution shells. Xtriage does not suggest merohedral twinning.
> Nevertheless, I extended my free flags in sftools from P6522 to P32 and cad'd them to amplitudes merged in spacegroup P32. Correspondingly, I expanded my model to a homotetramer and ran Refmac with amplitude based twinning. (Would this be a reasonable input to twin refinement?)
> From the output coordinates:
> REMARK 3 TWIN DETAILS
> REMARK 3 NUMBER OF TWIN DOMAINS : 4
> REMARK 3 TWIN DOMAIN : 1
> REMARK 3 TWIN OPERATOR : H, K, L
> REMARK 3 TWIN FRACTION : 0.269
> REMARK 3 TWIN DOMAIN : 2
> REMARK 3 TWIN OPERATOR : -K, -H, -L
> REMARK 3 TWIN FRACTION : 0.171
> REMARK 3 TWIN DOMAIN : 3
> REMARK 3 TWIN OPERATOR : K, H, -L
> REMARK 3 TWIN FRACTION : 0.258
> REMARK 3 TWIN DOMAIN : 4
> REMARK 3 TWIN OPERATOR : -H, -K, L
> REMARK 3 TWIN FRACTION : 0.302
> Does this establish twinning versus underestimated symmetry? And what do I need to know about my free-R? Did refmac assign a new flag? Whereas the output file's flags are all 1s and 0s, the input file had 0 ... 19. During the first run, Rfree dropped to <28%. But on a subsequent run, Rfree was stuck >30% when I used the initial job's output MTZ.
> Many thanks in advance for your helpful comments.
> Wolfram Tempel
>

--

ARKA CHAKRABORTY

CAS in Crystallography and Biophysics

University of Madras

Chennai,India