On Thursday, July 18, 2019 1:02:25 PM PDT Nicola Evans wrote: > > I have an unidentfied blob of density at a crystal contact region. I > > tried inputting a magnesium ion there, it was clearly incorrect but it > > improved the R-factors by 3, so I would really like to identify the > > correct molecule! Is there a tool to identify ligands in structures? I > > have tried the Phenix ligand identification tool to no avail (although > > it did find some nice horseshoe shaped PEG ions). I used glycerol and > > PEG400 as a cryo protectant, and identified a few glycerol and PEG > > molecules in other parts of the structure but not in this spot (well > > conditions: 0.2 M Magnesium chloride hexahydrate, 0.1 M BIS-TRIS pH > > 5.5, 25% PEG 3,350). As this is an the crystal contact region the > > molecule isn't likely to be biologically significant. The data have > > been solved to 1.9Å. I have attached a screenshot of the mysterious > > density. I would appreciate any suggestions! In addition, I am adding > > water molecules to this protein, and often there are what appear to be > > long chains. Are these likely to be long chains of ordered waters, or > > more PEG molecules? Thanks in advance for your help! Nicola
You might enjoy reading the recent paper by Kowiel et al (2018) "Automatic recognition of ligands in electron density by machine learning" https://doi.org/10.1093/bioinformatics/bty626 One of the more convincing examples they give (Fig 6D) is identification of a TRIS molecule. By coincidence the density in the this figure looks a lot like yours. cheers, Ethan -- Ethan A Merritt Biomolecular Structure Center, K-428 Health Sciences Bldg MS 357742, University of Washington, Seattle 98195-7742 ######################################################################## To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB&A=1
