Keith,
Thank you for bringing this issue to my attention.
I can confirm that PyMOL doesn't currently read SCALE records. In order
to generate correct crystal symmetry, it requires the input PDB coordinates to
be properly oriented and translated with respect to the crystal lattice origin
and axes. However, I think this is the default case with most of the standard
refinement programs. At the very least, PyMOL should print a warning if it
finds a SCALE record!
I'll see if we can't get SCALE handling in before the next release.
Cheers,
Warren
> -----Original Message-----
> From: Keith Refson [mailto:[email protected]]
> Sent: Wednesday, November 27, 2002 7:02 AM
> To: [email protected]
> Subject: [PyMOL] Pymol ignores SCALE records in PDB files
>
>
> Just to repeat the subject, it appears that pymol takes no account of
> the SCALE records in a PDB file.
>
> The built in assumptions of the orientation of the unit cell therefore
> gives an erroneous relationship between the unit cell and the atomic
> co-ordinates. The attached file demonstrates the problem.
> "Show->Cell" puts the long dimension of the cell perpendicular to the
> line of the atoms, rather than collinear with them as it ought to be.
> More seriously then, "symexp" gives a completely wrong expansion.
>
> HEADER UNKNOWN
> TITLE
> AUTHOR GENERATED BY XX2PDB (Keith Refson, 1998)
> CRYST1 5.024 5.024 5.024 39.69 39.69 39.69 P 1
> SCALE1 0.338511 0.000000 0.072121 0.00000
> SCALE2 -0.169255 0.293159 0.072121 0.00000
> SCALE3 -0.169255 -0.293159 0.072121 0.00000
> HETATM 1 H00 NON A 1 0.000 0.000 6.933 1.00
> 0.00 H
> HETATM 2 F00 NON A 1 0.000 0.000 5.792 1.00
> 0.00 F
> HETATM 3 F00 NON A 1 0.000 0.000 8.073 1.00
> 0.00 F
> HETATM 4 Na00 NON A 1 0.000 0.000 0.000 1.00
> 0.00 Na
> TER 4 NON A 1
> END
>
> sincerely
>
> Keith Refson
> --
> Dr Keith Refson,
> Building R3
> Rutherford Appleton Laboratory
> Chilton
> Didcot
> Oxfordshire OX11 0QX
> T: 01235 778023 K.Refson@
> F: 01235 445720 @rl.ac.uk
>
>
>
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