Hi all,
I have problems showing a EM structure in PyMol. When I open the PDB file 3J6J
in PyMol, the structure is shown very small in a diameter of about 1Ang. This
makes some representations like Cartoon or sticks unusable and comparison with
other structures impossible. I checked the file and it seems like the unit cell
is set to P1 with 1Ang dimensions in all directions:
CRYST1 1.000 1.000 1.000 90.00 90.00 90.00 P 1 1
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 0.010081 0.000000 0.000000 0.00000
SCALE2 0.000000 0.010081 0.000000 0.00000
SCALE3 0.000000 0.000000 0.012601 0.00000
I think that's were the problem lies. When I manually edited the PDB file and
replaced the 1.000 values in the CRYST1 record with the values decided by the
numbers in the SCALE records, the structure is shown correctly.So I think PyMOL
is not reading the SCALE record correctly. The same file is shown correctly in
other software like Coot or CCP4MG, so I think it is a Pymol related problem.
I am using Pymol 1.7.2.1 on MacOSX but had the same problem on a Windows
computer.
Bernhard
Bernhard C. Lechtenberg, PhD
Postdoctoral Fellow
Riedl Lab
Sanford-Burnham Medical Research Institute
10901 North Torrey Pines Road
La Jolla, CA 92037, USA
Phone: 858.646.3100 x 4216
Email: blechtenb...@sanfordburnham.org<mailto:blechtenb...@sanfordburnham.org>
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