If you run scala after data integration, ( and thats a good idea whether 
you have used any integration software - just get out the unmerged 
scaled file - feed it through pointless to get useful info there, and 
then scala/truncate to get more useful graphs and analysis)   there isa 
an option to extract the freeR set from a previous data set. That is 
highly recommended if you have such data.

Eleanor


On 11/21/2011 11:48 PM, Dale Tronrud wrote:
>     I'll jump in here, and avoid the question entirely.
>
>     Since running MR on an isomorphous crystal gives the same answer as just
> stuffing in the model and running some rigid body refinement, however you decide
> to handle your R free flags, you should do the same thing in both cases.  The
> model is the same.
>
> Dale Tronrud
>
> On 11/21/11 14:47, Michael Thompson wrote:
>> ----- Forwarded Message -----
>> From: "Michael Thompson"<[log in to unmask]>
>> To: "e dodson"<[log in to unmask]>
>> Sent: Monday, November 21, 2011 11:30:17 AM GMT -08:00 US/Canada Pacific
>> Subject: Re: [ccp4bb] LESS MR pleae.. 1.95A, different phase
>>
>> A question regarding the plea for less MR (which I support):
>>
>> There have been several recent instances in which I have used the solution of an isomorphous structure to do rigid body refinement for a new crystal (as described by Eleanor). It has always produced good results. My question is about how to best handle the free set of reflections when doing this? I have heard a number of differing opinions about whether or not it is important to carry the freeR flags from the original structure over to the new data set. I have heard equally convincing arguments from both sides, so my young and impressionable mind does not know who to believe. I was hoping I could get an opinion from the "advocates for less MR."
>>
>> Sorry for hijacking this thread, but hopefully it will provide some insight that is relevant to the original post.
>>
>> Thanks!
>>
>> Mike
>>
>>
>>
>>
>> ----- Original Message -----
>> From: "Eleanor Dodson"<[log in to unmask]>
>> To: [log in to unmask]
>> Sent: Monday, November 21, 2011 2:23:21 AM GMT -08:00 US/Canada Pacific
>> Subject: Re: [ccp4bb] LESS MR pleae.. 1.95A, different phase
>>
>> Just a plea for less molecular replacement.
>>
>> If you get a new crystal of a known protein with the  same cell
>> dimension as youur old crystal, the most likely scenario is that it has
>> the same group, and you really should not try MR - use the previous
>> solution as input to do rigid body refinement, and then
>>    a) the R factor will tell you if this is a reasonable hypothesis (it
>> usually is..) and
>> b) you dont have this awful problem of not being able to compare the
>> solutions..
>>
>>    Eleanor
>>
>> On 11/20/2011 03:57 PM, Napoleão Valadares wrote:
>>> Thank you all for the replies. Felix Frolow, Dan Leahy, Hans
>>> Brandstetter, Boaz Shaanan and Tim Gruene you really helped a lot.
>>>
>>> I think I understand it now, I always thought the "one ring to rule them
>>> all" translated in the crystallography realms to "one origin to rule
>>> them all". That probably means I have a long road in front of me.
>>>
>>> I'm still half confused, I definitely need to read more, as much as I
>>> read about symmetry and space groups I never seem to improve or get a
>>> better understanding, but I'll keep trying.
>>>
>>> About the same origin:
>>> The pdbs of both Solution-1 and Solution-2 present the same space group
>>> and cell, as observed opening the pdbs as text files or in pymol. When I
>>> open both maps on coot they are not superposed but present the same cell
>>> and origin.
>>>
>>> If I open both solutions on pymol they clash. If I generate the symmetry
>>> mates of both solutions none of them are superposed, instead they clash.
>>> But I think they are related as you all pointed, I'll check it out.
>>>
>>> Thank you all for your kind answers and your patience with a beginner.
>>> Regards from a sunny Brazil,
>>> Napo
>>>
>>>
>>> On 11/20/2011 2:58 AM, Felix Frolow wrote:
>>>> Napoleao,
>>>> It is so called alternative origins play a game with you. You do not
>>>> change your structure by shifting 1/2 translation (or even combination
>>>> of these translations)
>>>> into directions of the main axes of your unit cell. Structure factors
>>>> after this operation stay the same, however phases change
>>>> systematically, producing however the same
>>>> map features.
>>>> Would I be a begin crystallographer now, I would read a bit more old
>>>> fashioned books
>>>> on crystallography such as probably Jensen and Stout…
>>>> FF
>>>> Dr Felix Frolow
>>>> Professor of Structural Biology and Biotechnology
>>>> Department of Molecular Microbiology
>>>> and Biotechnology
>>>> Tel Aviv University 69978, Israel
>>>>
>>>> Acta Crystallographica F, co-editor
>>>>
>>>> e-mail: [log in to unmask]<mailto:[log in to unmask]>
>>>> Tel: ++972-3640-8723
>>>> Fax: ++972-3640-9407
>>>> Cellular: 0547 459 608
>>>>
>>>> On Nov 20, 2011, at 07:42 , Napoleão Valadares wrote:
>>>>
>>>>> Hello,
>>>>> I'm observing a very strange phenomena (at least to me, I'm a
>>>>> beginner). It is related to symmetry (I think).
>>>>>
>>>>> I got a data set at 1.95A (I/Sigma 3.5, R-Factor and R-meas<  35% in
>>>>> the last shell) and a partially refined solution with R/Rfree 22/24,
>>>>> 166 aminoacids observed and around 30 solvent molecules. I'll call
>>>>> this Solution-1. The refinement was smooth, the densities were very
>>>>> clearly "asking" for the correct missing side chains and the map
>>>>> looks good.
>>>>>
>>>>> The space group I'm using is P212121, pointless and XDS agree with
>>>>> that (but me and pointless both have a long history of being wrong
>>>>> about space groups). Phenix.xtriage says there's no twinning.
>>>>>
>>>>> I took Solution-1 and used it as a template in a molecular
>>>>> replacement in the same space group (P212121) using the same mtz as
>>>>> the one used to refine the template. I got a different (not
>>>>> superposed in space) solution (called Solution-2, scores by Phaser
>>>>> RFZ=24.2 TFZ=33.0 PAK=0 LLG=1413 LLG=1899) that was readily refined
>>>>> in Phenix to R/Rfree 24/26 without any solvent molecule.
>>>>>
>>>>> - The solutions are not superposed in space, although they are
>>>>> near-identical and can be superposed yielding a C-alpha rmd =0.001.
>>>>> - Both structures present VERY similar density maps. The maps are not
>>>>> superposed in space, but when you "run the chain" in one map in Coot
>>>>> and do the same in the other it they the present exactly the same
>>>>> features. It is impossible to ignore their similarities.
>>>>> - Both structures and maps present the same origin and unit cell.
>>>>> - If I add to Solution-2 the equivalent solvent molecules of
>>>>> Solution-1 (I did this by superposing Solution-1 to Solution-2 then
>>>>> copy/pasting the solvent molecules), the R/Rfree become 22/24. This
>>>>> is a clear indication that the solutions are related.
>>>>> - I can't find any MR solutions using the same template and space
>>>>> groups P222, P2221 and P21212.
>>>>>
>>>>> How two different sets of phases can yield maps with the same
>>>>> features? What is happening, wrong space group? I have a feeling my
>>>>> lack of experience is the problem.
>>>>> Thank you.
>>>>> Regards,
>>>>> Napo
>>>>
>>>
>>>
>>