Dear crystallographers!
My basic question is, how can electron density maps be moved along with
the
respective PDB coordinates?
I would like to superimpose two structures from different space groups
(P21
and P212121) along with some
omit ligand density in the active center to later highlight the
different
binding sites of the ligands in the two crystal
forms using PyMol. How is this to be done?
I tried to superimpose structure A onto B with LSQ (worked of course)
and
move the omit map from A along
using the program MAPROT with the EULER angels and TRANSlation values
from
LSQ. However,
the moved omit map is never not even close to the ligand in the
superimposed
structure. What am I doing wrong?
2nd example:
When I do this with 2 datasets from the same spacegroup (P212121, highly
unisomorphous datasets) it is also not working
as I would expect it. However, I found a solution here. If I invert all
EULER angles and TRANSlation values from the
superposition of A-> B (i.e. the opposite movement B->A - right?), then
the
moved density from A fits the moved ligand from A nicely again. This
does
not work in the above case with different space groups.
How can this be explained? Is MAPROT not the correct program for this
purpose?
Tanks in advance,
Matthias
****************************************************
Dr. Matthias Zebisch
Universität Leipzig
Biotechnologisch-Biomedizinisches Zentrum
Strukturanalytik von Biopolymeren
Deutscher Platz 5
04103 Leipzig
Germany
Phone: 0049-341-97-31323 (lab) -31312 (office)
Fax : 0049-341-97-31319
email: matthias.zebi...@bbz.uni-leipzig.de
****************************************************
--- Begin Message ---
Dear crystallographers!
My basic question is, how can electron density maps be moved along with the
respective PDB coordinates?
I would like to superimpose two structures from different space groups (P21
and P212121) along with some
omit ligand density in the active center to later highlight the different
binding sites of the ligands in the two crystal
forms using PyMol. How is this to be done?
I tried to superimpose structure A onto B with LSQ (worked of course) and
move the omit map from A along
using the program MAPROT with the EULER angels and TRANSlation values from
LSQ. However,
the moved omit map is never not even close to the ligand in the superimposed
structure. What am I doing wrong?
2nd example:
When I do this with 2 datasets from the same spacegroup (P212121, highly
unisomorphous datasets) it is also not working
as I would expect it. However, I found a solution here. If I invert all
EULER angles and TRANSlation values from the
superposition of A-> B (i.e. the opposite movement B->A - right?), then the
moved density from A fits the moved ligand from A nicely again. This does
not work in the above case with different space groups.
How can this be explained? Is MAPROT not the correct program for this
purpose?
Tanks in advance,
Matthias
****************************************************
Dr. Matthias Zebisch
Universität Leipzig
Biotechnologisch-Biomedizinisches Zentrum
Strukturanalytik von Biopolymeren
Deutscher Platz 5
04103 Leipzig
Germany
Phone: 0049-341-97-31323 (lab) -31312 (office)
Fax : 0049-341-97-31319
email: matthias.zebi...@bbz.uni-leipzig.de
****************************************************
--- End Message ---
