We addressed some of these electrostatics problems (Xray artefact like presence
of ions, crystal packing, etc) a long time ago. Feel free to look at:
Improving macromolecular electrostatics calculations.
Nielsen JE, Andersen KV, Honig B, Hooft RW, Klebe G, Vriend G, Wade RC.
Protein Eng. 1999
Edit your XDS.INP file to look like this:
!JOB= XYCORR INIT COLSPOT IDXREF
JOB=DEFPIX INTEGRATE CORRECT
Then rerun ads and be happy thereafter.
and RTFM !
Jürgen
..
Jürgen Bosch
Johns Hopkins University
Bloomberg School of Public Health
Department of Biochemistry Molecular
Hi Lu
Mosflm indexes your image using all defaults without any problems ;-)
XDS shouldn't have any difficulties with indexing this.
I suspect your crystal only diffracts to ~3.0 - 3.5 Å so you could do a better
experiment by moving the detector back to ~ 900mm...
BUT - PLEASE don't attach
Hi LU,
the reason why IDXREF is not indexing smoothly is that the spot positions in
your SPOT.XDS are not very meaningful - you pick up a lot of noise! I plotted
your SPOT.XDS using
%%:-/tmp/luo% gnuplot
gnuplot set size square
gnuplot set out tmp.png
gnuplot set term png nocrop medium size
Dear Jürgen and Lu,
I am not sure IDXREF found the correct solution (taken from IDXREF.LP):
* INDEXING OF OBSERVED SPOTS IN SPACE GROUP # 3 *
2372 OUT OF 40947 SPOTS INDEXED.
3 REJECTED REFLECTIONS (REASON: OVERLAP)
38572 REJECTED REFLECTIONS (REASON: TOO FAR FROM
Dear all,
I am trying to model a full-length double-domain protein in dimer. The
structure of both N and C terminal domains are known and the linker region
of 5 residues are present in both structure (the linker might be flexible
though). The N-terminal domain's structure is also a dimer, which
