Dear All,
I would like to add my 5 cents to partly answer Eugene's questions about
the script, and to follow up on Eleonor's mentioning of Zbsyzek and the
rules for placing macromolecular structures in the crystal lattice.
For the last couple of years, we have been routinely using the ACHESYM
server for standardized placement of macromolecular models in the unit
cell cell (http://achesym.ibch.poznan.pl/) for all structure before
depositing them. It works great.
The following paper describes the server.
Kowiel, M., Jaskolski, M. & Dauter, Z. (2014). ACHESYM: an algorithm and
server for standardized placement of macromolecular models in the unit
cell. Acta Cryst. D70, doi:10.1107/S1399004714024572.
Dauter Z. On optimal placement of molecules in the unit cell. Acta
Crystallogr D Biol Crystallogr. 2013 May;69(Pt 5):872-8. doi:
10.1107/S0907444913002722. Epub 2013 Apr 19.
Ivan
With best regards,
Ivan Shabalin, Ph.D.
Research Scientist,
Department of Molecular Physiology and Biological Physics,
University of Virginia,
1340 Jefferson Park Avenue, Pinn Hall,Room 4223,
Charlottesville, VA 22908
https://www.linkedin.com/in/shabalinig/
https://minorlab.org/person/ivan_s/
On 11/10/19 06:49, Eugene Osipov wrote:
Dear Eleanor,
From PDB files I see that the structures were solved by molecular
replacement using pdbid 1gci as a starting model. It is hard to say
definitely without the linked paper but may be the depositors made the
same error that I did some time ago: they solved both structures using
molecular replacement instead of running rigid body refinement for
follow up structure.
Actually, the issue with different origins is pretty common in pdb. For
example, I searched pdb for isomorphous lysozyme structures in P43212
with unit cell dimensions a=b=78.5-79.3 and c=36.5-37.3 and have found
121 structures. I picked 6 random structures and only 2 of them have the
same origin.
By the way, may be someone has a script to move several isomorphous
structures to the same origin and rename chains according to reference
structure?
пт, 8 нояб. 2019 г. в 14:02, Eleanor Dodson
<0000176a9d5ebad7-dmarc-requ...@jiscmail.ac.uk
<mailto:0000176a9d5ebad7-dmarc-requ...@jiscmail.ac.uk>>:
I have just downloaded two isomorphous coordinates from the pdb
5arb and 5arc deposited by the same team
Tried to compare and they are on different origins.
I know it doesnt affect the crystallography
It is easily corrected
BUT it seems bad practice to me
Eleanor
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--
Evgenii Osipov
Laboratory for Biocrystallography,
Department of Pharmaceutical Sciences,
KU Leuven O&N2
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