You know what? Scratch what I said. As Mark says, there isn't any 2Fo-Fc density, which is suspicious.
However, I would still model what may fit in it, with appropriate occupancy, based on the symmetry. To be doubly sure. I have, in the past, used ProDRG<http://davapc1.bioch.dundee.ac.uk/prodrg/submit.html>for obtaining pdf, topology and parameter files for ligands. ARP/wARP can be used for a first fit of ligand into density. You may find appropriate fatty acid pdb-top-param files already in the HIC-UP <http://xray.bmc.uu.se/hicup/> database. I would do a quick search for a fatty acid of an appropriate length. If it is truly spurious density as I suspect it is, you'll see negative density lighting up your screen despite using appropriately low occupancy. Good luck! Sangeetha. On Sun, Nov 4, 2012 at 8:17 PM, Sangeetha Vedula <[email protected]>wrote: > Could it be a fatty acid? It looks like it has a (hydrophobic?) tail with > a (charged?) head. Partially occupied perhaps, as they're so close together. > > > On Sun, Nov 4, 2012 at 7:38 PM, yogesh khandokar < > [email protected]> wrote: > >> Dear All >> >> I am working on an enzyme which involved in fatty acid biosynthesis. We >> solved the crystal structure of it. Biological unit of this enzyme is >> Hexamer and showing extra electron density in the center of Hexamer. >> Wincoot software doesn't recognize this extra electron density as water >> molecules/ substrate. >> >> My question is:Is there any way to find the molecules responsible for >> extra electron density? >> >> Picture is attached with email. >> >> Thanks in advance for your comments. >> >> Regards >> -- >> Yogesh Khandokar >> PhD Student >> School of Biomedical Sciences >> Charles Sturt University >> Wagga Wagga, NSW, >> Australia >> http://www.csu.edu.au/faculty/science/biomed/ >> >> >
