The choice of origin is completely arbitrary as far as I can see - any
or all of the alternates satisfies an MR search equally well..
Eleanor
Kolstoe S.E. wrote:
> Thanks for the help everyone.
>
> I followed Jan's suggestion of running lsqkab which gave a translation
> vector in fractions of cell edge of 0.5 0.5 0.5 between the two
> solutions. I then checked Paul's link to the alternative origins
> spacegroup page on the ccp4 site and sure enough one of the alternatives
> for P21212 is 0.5 0.5 0.5
>
> Are phaser and molrep set up to use different conventions on this or is
> the choice a bit more complex?
>
> Thanks once again to everyone who responded.
>
> Simon
>
>
>
> -----Original Message-----
> From: CCP4 bulletin board [mailto:[log in to unmask]] On Behalf Of
> Ian Tickle
> Sent: 08 August 2007 17:06
> To: [log in to unmask]
> Subject: Re: [ccp4bb] mr query
>
> Hi Simon
>
> You didn't say whether you have just 1 mol/a.u. or more than one. In
> the latter case you can get the effect you observe because as well as
> considering possible origin shifts you also have to consider the
> possibility that say the A and B molecules have been switched, i.e. like
> the origin shifts the labels A & B assigned by the MR program are
> completely arbitrary. I had a similar case with 2 mols/a.u. where I got
> solutions from different MR programs with identical R factors around 20%
> and the molecules were apparently shifted by about 3 Ang relative to
> each other. As soon as I switched the A and B labels in one of the
> solutions it was obvious that the solutions were in fact identical (this
> happened because in that particular case the A-B translation vector was
> almost 1/2 of a lattice translation).
>
> However if you have only 1 mol/a.u. then this doesn't help - in which
> case I'm as baffled as you, sorry!
>
> Cheers
>
> -- Ian
>
>
>> -----Original Message-----
>> From: [log in to unmask]
>> [mailto:[log in to unmask]] On Behalf Of Kolstoe S.E.
>> Sent: 08 August 2007 16:51
>> To: [log in to unmask]
>> Subject: mr query
>>
>> Dear ccp4bb,
>>
>> In searching for a mr solution I ran both phaser and molrep,
>> with both programs finding nice solutions in P21212 (cell
>> 81.083 104.435 109.732 90.00 90.00 90.00, resolution
>> 2.65A). For various reasons I refined the phaser and molrep
>> solutions separately, and both behaved in exactly the same
>> way giving R=0.24, Rfree=0.28 after adding ligands, mutations
>> etc. Today I decided to compare the two models (which I
>> figured were exactly the same) however found that the
>> asymmetric units did not superimpose. Normally this is just a
>> case of each mr program finding a different asymmetric unit
>> in the same cell, however this time there is a distinct clash
>> between the two solutions with about 50 atoms overlapping.
>> After playing around with various symmetry equivalents I have
>> found that the difference between the solutions is
>> approximately a 30A translation along the x axis. As there is
>> no signs of any twinning, and both solutions behave in
>> exactly the same way in refinement, is this a case of phaser
>> and molrep using different origins or is there something more
>> insidious going on?
>>
>> Thanks for any advice,
>>
>> Simon
>>
>>
>>
>
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