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:k...@isise.rl.ac.uk]
Sent: Wednesday, November 27, 2002 7:02 AM
To: pymol-users@lists.sourceforge.net
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.
HEADERUNKNOWN
TITLE
AUTHORGENERATED BY XX2PDB (Keith Refson, 1998)
CRYST15.0245.0245.024 39.69 39.69 39.69 P 1
SCALE1 0.338511 0.00 0.0721210.0
SCALE2 -0.169255 0.293159 0.0721210.0
SCALE3 -0.169255 -0.293159 0.0721210.0
HETATM1 H00 NON A 1 0.000 0.000 6.933 1.00
0.00 H
HETATM2 F00 NON A 1 0.000 0.000 5.792 1.00
0.00 F
HETATM3 F00 NON A 1 0.000 0.000 8.073 1.00
0.00 F
HETATM4 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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