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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 > <[log in to unmask] > <mailto:[log in to unmask]>>: > > 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 > > > > ------------------------------------------------------------------------ > > To unsubscribe from the CCP4BB list, click the following link: > https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB&A=1 > > > > -- > Evgenii Osipov > Laboratory for Biocrystallography, > Department of Pharmaceutical Sciences, > KU Leuven O&N2 > > ------------------------------------------------------------------------ > > To unsubscribe from the CCP4BB list, click the following link: > https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB&A=1 > ---- ######################################################################## To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB&A=1