RE: [PyMOL] Pymol ignores SCALE records in PDB files

[DeLano, W. <wa...@su...>]

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:kr...@is...]
> Sent: Wednesday, November 27, 2002 7:02 AM
> To: pym...@li...
> Subject: [PyMOL] Pymol ignores SCALE records in PDB files
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> Just to repeat the subject, it appears that pymol takes no account of
> the SCALE records in a PDB file.
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> 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.
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> 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 =20
> 0.00           H
> HETATM    2  F00 NON A   1       0.000   0.000   5.792  1.00 =20
> 0.00           F
> HETATM    3  F00 NON A   1       0.000   0.000   8.073  1.00 =20
> 0.00           F
> HETATM    4 Na00 NON A   1       0.000   0.000   0.000  1.00 =20
> 0.00          Na
> TER       4      NON A   1
> END
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> sincerely
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> Keith Refson
> --=20
> Dr Keith Refson,=20
> Building R3
> Rutherford Appleton Laboratory
> Chilton
> Didcot
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> T: 01235 778023		K.Refson@
> F: 01235 445720		@rl.ac.uk
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