You also need to change the cell to the new structure - if there is a
small change in cell dimensions and the parent is far from the origin,
then this can make for a sizeable error.
PDBSET accounts for this for you providing you give it the new cell and
symgen x,y,z: the old coordinates are converted to fractions then
converted back to As according to the new cell..
( By theway this is one reason why MR programs should output a pdb as
closse to the origin as possible - not apply a shift of 0.99 0.99 0.99 ..)
An alternative is run a MR program such as Phaser or Amore which allows
you to do the rigid body refinement as a seperate step , starting from a
solution Euler 0 0 0 Translation 0 0 0 (for Phaser ) or
Euler 0 0 0 Translation -COMx -COMy -COMz for Amore. (run TABLING with
the NOROTATE option and see output for COM coordinates. )
I believed Amore has the best r igid body refinement algorithm around -
havent tested Phaser really..
Eleanor
this providing Shane Atwell wrote:
When solving structures that are the same crystal form as a parent,
what's the best way of getting or moving the solution to the same
position as the parent? This is for cases where a typical rigid body
refinement isn't sufficient to pull out the solution.
It is not very convenient to look at the parent and the solution and
then fix the solution using pdbset symgen, at least for dozens or
hundreds of structures.
I've tried using beast to do the MR in a small box around the parent
solution, and it works, but takes a long time even for a 'small'
search area (e.g. 10 degrees and 2 Angstroms).
Its possible that doing the rigid body refinement w/ lower res data
could pull in solutions that are further off, but I doubt it would be
very robust..
It also seems possible to use contact or a similar program to find
which symmetry molecule of the solution 'clashes' with the parent
solution. I'm toying with this, but haven't gotten it to work yet.
Short of custom modification of the MR program, is there something
available that I'm missing?
Shane Atwell
begin:vcard
fn:Eleanor Dodson
n:Dodson;Eleanor
email;internet:[EMAIL PROTECTED]
tel;work:+44 (0) 1904 328259
tel;fax:+44 (0) 1904 328266
tel;home:+44 (0) 1904 424449
version:2.1
end:vcard
