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Hi Uhnsoo,
AMoRe will not run the translation function for the **first** body (an
hetero-dimer in your case) because in P1 the origin is arbitrary and
hence fixed by the first rotation solution. Now, if you think that the
first solution from the rotation function list is not good you can
manually fix another solution in the list and go on. The translation
function will be then calculated for the second and successive bodies
(other hetero-dimers in your case)
I would say that your solution from phaser looks quite compelling, but
then it's strange that molrep didn't come with the same solution. When
you say that your solution from phaser has 4 molecules, do you mean the
four expected hetero-dimers or just two hetero-dimers? If the latter,
perhaps your solution will not refine better because it is too
incomplete. In this case, you could still try to use your partly refined
model to find the other two hetero-dimers.
Cheers,
Miguel
En/na [EMAIL PROTECTED] ha escrit:
> Dear all,
>
> Recently, I've gotten a 3.1A data set with a P1 space group. Based on a
> Mattchew
> coefficient, I have 4 hetero-dimer molecules in one asymmetric unit.
> Because one
> of the dimers was known already, I tried MR with a program Phaser and
> molrep
> (Amore doesn't calculate a translation function with a P1 space group).
> Phaser gave
> me a reasonable solution with Z-score closed to 20 and LL-gain over
> 900(molrep
> didn't give me a good solution), and that solution has 4 molecules with
> quite
> reasonable packing with local 2-fold symmetries. I also ran Phaser with
> different wavelength ranges with different truncated forms, and always the
> solutions were the same. However, when I calculated the map, the map was
> still
> messy and I couldn't see a clear density of the other molecules. I also
> ran a
> rigid body refinement and a restrained refinement with different programs
> (refmac and cns), but the R factor didn't drop. I ran DM with ncs
> averaging and
> solvent flattening, still the map wasn't improved. At this moment, we
> are still
> sure that our data set has a P1 space group with good statistics and the
> solution from phaser is quite reasonable.
>
> Is it possible that P1 space group can be a problem during MR? Do you
> think the
> solution from Phaser is just wrong or did I miss something?
>
> Any suggestions will be helpful to me.
>
> Thanks,
>
>
>
>
> uhnsoo
>
- --
Miguel Ortiz Lombardía
Centro de Investigaciones Oncológicas
C/ Melchor Fernández Almagro, 3
28029 Madrid, Spain
Tel. +34 912 246 900
Fax. +34 912 246 976
e-mail: [EMAIL PROTECTED]
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Et ainsi ne pouvant faire que ce qui est juste fût fort, on a fait que
ce qui est fort fût juste.
Blaise Pascal, Pensées
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