Gregory Bowman wrote:
Hi all,
We have several primitive monoclinic datasets for the same protein with various ligands,
with essentially the same unit cell parameters. We would like to have these with the
molecules/density oriented the same way for easy comparison, but as chance would have it,
some have effectively the opposite "k" index, which of course puts these
molecules/density (relatively) upsidedown. I was wondering how people typically deal with
this. I found what I believe to be the answer of reindexing monoclinic h, k, l to -h,
-k, h+l to keep the system right handed and flip k. For this it seems that SFTOOLS would
be appropriate? Is this reindexing commonly done at the stages of integration (altering
rotx roty rotz in HKL2000) or scaling?
Thanks,
Greg
If you want to redo in HKL, look at the denzo/scalepack manual,
scalepack scenario 5, reindexing.
I think your case is the first example, "switch a and c in p21"
HKL MATRIX
0 0 1 [reindexing matrix: h -> l]
0 -1 0 [this is -1 to keep determinant = 1]
1 0 0 [l -> h]
If you just want to reindex the data, you can use the previous scalepack
output (.sca) as input. If you rescale the denzo output files (.x)
with this HKL matrix, then in the log file, just below the unique
occurance of the word "mosaicity" in the file, is a line (or several
lines if "fit batch") which gives the post-refined missetting angles
and cell param, which can be edited into the corresponding lines of
integ.inp if you want to re-integrate in the re-indexed setting.
(I don't know if there is any good reason to do so, however).
