The new pointless which is the underlying program for the "Test 
Alternate Indexing" task from the CCP4-6.0.2 GUI  works brilliantly for 
matching 2 data sets.
However in P21212 if a not-equal b not-equal c it is hard to confuse them..

 Like Tassos I think you should start your experiment by merging all 
data sets with CAD - checking they are isomorphous with SCALEIT ( Exptl 
Phasing tasks) , worrying a lot if they are not! then using the 2.3A 
data for phase extension from the 2.7A exptl phases. DM with averaging 
and phase extension will improve your map a lot, and maybe you can build 
the other 30%
  Eleanor

PS - as a crystallographic educator I am a bit upset that this isnt the 
norm for experimental phasing - phase extension is brilliant!! and not 
using it is rather reminiscent of self flagelation..

Anastassis Perrakis wrote:
> Hi -
>
> Its not clear to me if the 2.3 A dataset is from a different crystal, 
> if it has the same space group as the 2.7 A dataset and if it is 
> isomorphous, and how the 'jump' from the 2.7 A dataset to the 2.3 A 
> dataset has been done. I can think of quite a few ways to do that 
> transition, and each way can carry its own problems.
>
> Maybe its worth clarifying these in more detail.
>
> I also have to say that (for once!) I dont agree with Kay. I have 
> tried in the past to refine against datasets processed with different 
> programs, and I know people that do that a lot; the differences are 
> minor at best (1-2 % Rfree, mostly differences are in the anomalous 
> signal quality). Thus I dont think its processing but a mistake in the 
> settings or somewhere else something that went clearly wrong 
> (different origin ?). Anyway, i am not sure about that either, since 
> Satinder says that the model does fit the density (which density 
> though ? Also not clear).
>
> BTW, assuming that the two datasets are from different non-isomorpous 
> crystals, thats what I would be tempted to try and do:
>
> 1. Use 'phaser' to do a molecular replacement of the 70% complete 
> model to the 2.3 A dataset
> 2. Use 'cad' to combine the output mtz file of 'phaser' with phases 
> and weights, with you SAD phases and weights, plus Fobs of both datasets.
> 3. Use dmmulti to do 'multi-crystal averaging' using the molecular 
> replacement phases of the 2.3 A dataset and the 2.7 A SAD phases. Also 
> use the NCS. That must result to a good 2.3 A map.
> 4. Use ARP/wARP to autotrace the 2.3 A map with the 2.3 A fobs.
>
> I should also add that if I had a 2.3 A native and a 2.7 A SAD map in 
> NON-isomorphous crystals in the first place, I would use DM-multi 
> directly,  
> even without phases for the 2.3 A map. That has worked beautifully for 
> me in the past. Anyway - too late for that now since you have a model.
>
> Last but not least if the 2.3 A dataset and the 2.7 A dataset are 
> isomorphous, I would most definitely have tried phasing using both of them
> Especially if one had eg Se and one did not (the best SAD experiment 
> will give you 6 to 7 e to use; Se-S has 18 e. why not use them if you 
> can ??
> yes, SAD might sometimes be the best map as many people have shown 
> over the last few years, 
> but also sometimes the Se-derivative - Native has lots and lots of 
> info and using all info can give better maps when non-isomorphism is 
> not a problem.)
>
> May I also assume that when you are sure of the space group that means 
> you put it through x-triage and its not a disguised P21 twin, 
> as many P21212 cases I have seen.
>
> Tassos
>
> On Jul 27, 2007, at 2:19, Satinder K. Singh wrote:
>
>> Hello,
>>  
>> I have a SAD data set to 2.9A and a native data set on the same 
>> protein to 2.3A. I have built 70% of the model (polyalanine) into the 
>> SAD experimental map that has been subjected to 2-fold NCS averaging 
>> and phase-extended to 2.3 A. From the maps, the model looks like it 
>> fits the density fine, but when I try to refine (either rigid-body or 
>> positional refinement in REFMAC or simulated annealing in CNS), I get 
>> an R-factor of ~60%, worse than random. Similarly, a SigmaA run 
>> ("combine isomorphous phase with partial structure") on the model 
>> yields an R-factor of ~60%. However, when I run DM on the 
>> original phase-combined file (before NCS averaging and phase 
>> extension) in omit mode, I get an R-free of 34.6%, which suggests 
>> that the map files itself is okay.
>>  
>> I also checked the space group of the processed data, and it is 
>> definitely P21212.
>>  
>> Does anyone have any suggestions of what I may be doing wrong?
>>  
>> Thanks in advance for your help.
>>  
>> Kind regards,
>> Satinder
>>
>