SCALEn records enable conversion of *arbitrary* input PDB coordinates into correct fractional coordinates. However, PyMOL requires correct orthogonal coordinates for application of crystal symmetry. So, CRYST1 crystal lattice parameters are then used to generate correct orthogonal PDB coordinates from the SCALEn-derived fractional coordinates.
Note that ORIGXn is effectively redundant with SCALEn / CRYST1. I’m not sure why PYMOL chooses to apply SCALEn and CRYST1 instead of using ORIGXn, but it may be that SCALEn is more common than ORIGXn in the PDB.
PyMOL brings its use of SCALEn to your attention because those matrices are bogus in a surprising number of cases.
[mailto:email@example.com] On Behalf Of Wolfgang Meyer
Sent: Monday, May 14, 2007 3:14 AM
Subject: [PyMOL] why orthogonal coordinates are re-computed for 4hhb.pdb
When I open PDB model 4hhb.pdb in PyMol:
HEADER OXYGEN TRANSPORT 07-MAR-84 4HHB 4HHB 3
COMPND HEMOGLOBIN (DEOXY) 4HHB 4
ObjectMolecule: Read secondary structure assignments.
ObjectMolecule: Read crystal symmetry information.
Symmetry: Found 2 symmetry operators.
ObjectMolReadPDBStr: using SCALEn to compute orthogonal coordinates.
CmdLoad: "d:\pdbs\4hhb.pdb" loaded as "4hhb".
it says: "using SCALEn to compute orthogonal coordinates."
So why orthogonal coordinates are re-computed for 4hhb.pdb ?
Besides, in PDB format document it says:
The SCALEn (n = 1, 2, or 3) records present the transformation from the orthogonal coordinates as contained in the entry to fractional crystallographic coordinates.
It seems using SCALEn and coordinates presented in PDB file one should get fractional coordinates in the end.
I am using pymol version 0.99rc6 and my OS is window XP SP2.
Thanks for your answer!