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, Napolećo 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 , Napolećo 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
>>
>
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