molecular replacement question

Phil Jeffrey phil at xtreme1.mskcc.org
Sun Apr 2 18:12:33 EST 1995


In article <3lf28r$pnb at nntp.ucs.ubc.ca> ywchen at laue.biochem.ubc.ca (Y. W. Chen) writes:

>> I have a structure which has one molecule in the asymmetric unit of P6222.
>> ... I believe this monomer forms dimer related by a crystallographic 2-fold.
>> ... I would like to try using the dimer to search in P62.  
>> ... a way to restrict the cross-rotation search to be along a known axis.
>> ... I use the CCP4 suite ... ie AMORE, ALMN, POLARRFN, and X-PLOR as well.

Here's my 2c:

There are two potential types of dimers on P6<2>22 - the one along the 6<2>
and the other two-folds perpendicular to it.  Althogh it's probably not too
tough to work this out in Crowther-Euler angles, the easiest system to think
about this in (for me) are the spherical polar angles in POLARRFN.

First, you need to orient your dimer model such that the dimer axis is parallel
to Z (actually two models - the "up" model and the "down" model). Then the
set of angles to search would be:

Phi, Psi, Kappa
 0,   0,    *          for the 6<2> axis
 0,  90,    *	       for the 22 axes perpendicular to the 6<2>

for each model. You would want to use NCODE=1 or NCODE=5, and check that Phi=0
and not Phi=30 for the second case. (two fold along X or 30 degrees to X).

Alternatively, if you can determine the range of Crowther Eulerian angles 
that correspond to these polar angles, you can do a pseudo-2D search using a
translation function program like BRUTE (Fujinaga & Read, my personal favorite)
where one of the dimensions is the rotation about the dimer axis and the
other is the translation along the dimer axis.  Especially in the case of a
poor model, this might be what you need to do to solve the structure.

Caveat: never done this myself, and it's been about 8 years since I used
POLARRFN.

Regards,
Phil Jeffrey

--
-------------------------------------------------------------------------------
| Phil Jeffrey                                  |                             |
| X-ray/Computer Manager, Crystallography Lab   | If you lie to the compiler, |
| Memorial Sloan-Kettering Cancer Center, NYC   | it will get its revenge     |
| phil at xray2.mskcc.org, p-jeffrey at ski.mskcc.org |     - Henry Spencer         |
| Ph: (212) 639 2189   Fax: (212) 717 3066      |                             |
-------------------------------------------------------------------------------




More information about the Xtal-log mailing list