There was a paper/comment in Acta Cryst by Zbigniew Dauter "the asymmetric unit should be close to the origin".
The uncomfortable source is most probably that the result of a molecular replacement is sometimes an asymmetric unit "elsewhere" , origin shifts etc. Nice weekend Winfried Hinrichs ---------------------------------------------------------------------- Dr. rer. nat. Winfried Hinrichs Professor and Chair of Biochemistry, Emeritus University of Greifswald Institute for Biochemistry Felix-Hausdorff-Str. 4 D-17487 Greifswald, Germany E-mail winfried.hinri...@uni-greifswald.de http://orcid.org/0000-0002-0435-4565 ---------------------------------------------------------------------- Am Sonntag, den 10-11-2019 um 12:55 schrieb Frank Von Delft: Eleanor, whom are you grumbling at? If it's at the depositors, here's a counter-grumble: How would a depositor even know???? * know that it's "wrong" * know what definition of "wrong" to work towards * know that someone somewhere will care about this particular "wrongness" * know that visualisation or analysis software does not elegantly deal with this - it is after all 2019 already If I had to prioritise wrongnesses, I'd put top of the list that it is not as absolutely trivial as possible to get data into the public domain. Which means working hard (even harder!) to remove all arcane things from the ecosystem. Frank On 10/11/2019 11:49, 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. Bythe 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 : 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 ######################################################################## To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB&A=1
