Re: [ccp4bb] Identifying an unknown ligand

[Roger Rowlett]

Some context would be helpful (essential?). What's in the crystallization solution? What, if anything, is known about the protein of interest? What is the ligand interacting with (metal ions, hydrogen bonding donors/acceptors, charged residues, etc?), and what are the interaction distances? Do any of the atoms appear to be "heavy" or show anomalous scattering, if applicable, at the wavelength used?  etc. etc. -- Roger S. Rowlett Professor Colgate University Presidential Scholar Department of Chemistry Colgate University 13 Oak Drive Hamilton, NY 13346 tel: (315)-228-7245 ofc: (315)-228-7395 fax: (315)-228-7935 email: rrowl...@mail.colgate.edu Abhinav Kumar wrote: Hi, I am refining a structure and have a region of unmodeled density into which I am trying to fit a ligand. The identity of the ligand is not obvious, so I modeled a bunch of dummy atoms into the density. Could you please have a look at the map and pdb files and help me identify this ligand? Please see http://smb.slac.stanford.edu/~abhinavk/UNL/unl.html Thanks Abhinav Stanford Synchrotron Radiation Laboratory Joint Center for Structural Genomics Mail Stop 99 Phone: (650) 926-2992 Fax: (650) 926-3292