Biology Asked by Slowpoke on August 2, 2020
According to the PDB guide there are some coordinate translation matrices found in PDB file:
ORIGXn Transformation from orthogonal coordinates to the
submitted coordinates (n = 1, 2, or 3).
SCALEn Transformation from orthogonal coordinates to fractional
crystallographic coordinates (n = 1, 2, or 3).
MTRIXn Transformations expressing non-crystallographic symmetry
(n = 1, 2, or 3). There may be multiple sets of these records.
For example, in 10gs
complex from RCSB I see:
ORIGX1 1.000000 0.000000 0.000000 0.00000
ORIGX2 0.000000 1.000000 0.000000 0.00000
ORIGX3 0.000000 0.000000 1.000000 0.00000
SCALE1 0.012543 0.000000 0.001805 0.00000
SCALE2 0.000000 0.011055 0.000000 0.00000
SCALE3 0.000000 0.000000 0.014557 0.00000
MTRIX1 1 0.945333 0.099229 0.310644 -5.48795 1
MTRIX2 1 0.099832 -0.994906 0.013998 21.83043 1
MTRIX3 1 0.310451 0.017779 -0.950423 27.67516 1
I want to do 3D voxel reconstruction of some part of the complex stored in PDB. What is the purpose of those matrices, do I need to apply any of those translations to the coordinates stored in PDB to "standartize" the data and obtain the same coordinate system and same grid for different PDBs? Or they are just related to the data which was submitted by authors and are needed for inverse translation? Or something else? Thank you very much!
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