Hi Jeremy, Given the large number of different kinds of ligands that are observed (either from crystallization, purification conditions or endogenous), I think it will be really difficult to assign just by visual and manual comparison with a standard set, especially for inexperienced crystallographers.
Better to use modules like LigandFit in Phenix, which can use the Refmac ligand library or user-defined library to scan the putative ligand density in difference maps in the structure. If you want a nice overview of different common ligands that have been observed in ~3000 structures from PSI/Structural Genomics efforts (including a whole bunch of unidentified ligands), along with their PDB ids so you can see corresponding density, have a look at this paper: Acta Crystallogr Sect F Struct Biol Cryst Commun. 2010 Oct 1;66(Pt 10):1309-16. doi: 10.1107/S1744309110008092. Epub 2010 Jul 6. Ligands in PSI structures. Kumar A, Chiu HJ, Axelrod HL, Morse A, Elsliger MA, Wilson IA, Deacon A. Stanford Synchrotron Radiation Lightsource, SLAC National Accelerator Laboratory, Menlo Park, CA, USA. PMID: 20944227 http://www.ncbi.nlm.nih.gov/pubmed/20944227 Best, Debanu. -----Original Message----- From: CCP4 bulletin board [mailto:[email protected]] On Behalf Of ??? Sent: Tuesday, May 21, 2013 12:30 PM To: [email protected] Subject: [ccp4bb] list/library of most commonly co-crystallized ligands/solvents and/or their electron density shapes hi all, Sorry if this has been asked before. I wonder if there is an list or library of most commonly co-crystallized ligands(or solvent molecules) available? Better if the electron density maps of the ligands are also shown with different resolutions. That could help a lot for an inexperienced crystallographer (like me) to quickly identify extra electron densities in a new structure, by simply comparing the electron density shapes. I remember a few days ago somebody asked about a PEG electron density, which looks like a string of beads. If I knew that earlier, I could have modeled it in, instead of waters... Thanks, Jeremy
