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Dear all,
after following this discussion for the last few days, I feel that I
have to add my few cents worth, prompted by one of the last comments:
David Briggs schrieb:
...
Well done coot - any possible problem was immediately obvious.
However, other display programs I had to hand, such as Rasmol and PyMol
showed no problem.
...
Isn't the discussion also a question of the programs we all are using
and how they deal with the different potential representations of
"non-visible" atoms in the pdb-file ?
I know many programs that make trouble if atoms are missing (e.g., a Lys
truncated to Ala length). If the occupancy of the more distal atoms is
deliberately set to zero instead, all necessary information is there:
(1) no program can complain about missing atoms (and make it up from
nowhere), (2) due to the occupancy set to zero, it is clear that these
atoms are not visible and that the person responsible for the pdb-file
intentively deleted them from refinement and density calculation, (3)due
to zero occupancy, these atoms are not visible for R-factors, density
calculation etc., i.e., they do no harm and (4) such a file still allows
the clear distinction between large B-factors refined for residues which
are still somewhat visible in the density and those atoms that are not
visible and placed as "best bet".
I believe that this is the best solution to the "problem" and that the
real question is rather one of the representation by different programs.
(Don't hit me to hard for this statement - It's exaggerated on purpose
:-) - Of course many arguments can be made in either direction and all
of us have their own feelings about it.)
Best regards,
Manuel Than
--
**************************************************************************
Dr. Manuel E. Than
Protein Crystallography Group
Leibniz Institute for Age Research -
Fritz Lipmann Institute (FLI)
Beutenbergstraße 11
D-07745 Jena
Germany
Tel.: ++49 3641 65 6170
Fax.: ++49 3641 65 6335
e-mail: [EMAIL PROTECTED]
http://www.fli-leibniz.de/groups/than.php
