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:[EMAIL PROTECTED] On Behalf Of
Ian Tickle
Sent: 08 August 2007 17:06
To: [email protected]
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: [EMAIL PROTECTED]
[mailto:[EMAIL PROTECTED] On Behalf Of Kolstoe S.E.
Sent: 08 August 2007 16:51
To: [email protected]
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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