Andy, on the practical point of view, you can create such images using Pymol and the command 'carve'.
load composite_omit-ccp4.map, map-to-display, format=ccp4 isomesh mesh, map-to-display, 1.5, resi 45, carve=3 color blue, mesh this will display the map at 1.5 sigma, at 3 angstroms around the residue 45. it gives you nice clean maps and it's a nice trick to remove the noise in your density, with obvious ethic limitations... But if you carve 20A around your residue, you're safe. If i remember correctly, ligands create problems because of the HETAM in the PDb file but you can replace it with ATOM and it should work. the commands 'around' or 'expand' can achieve similar figures i believe. Check he pymol wiki for more infos. vincent ANDY DODDS wrote:
Hello, I was wondering what people used to generate difference map images of, say, a ligand in their structures? e.g. Figure 2a here http://journals.iucr.org/f/issues/2009/05/00/tt5012/tt5012.pdf Cheers, Andy
IMPORTANT WARNING: This email (and any attachments) is only intended for the use of the person or entity to which it is addressed, and may contain information that is privileged and confidential. You, the recipient, are obligated to maintain it in a safe, secure and confidential manner. Unauthorized redisclosure or failure to maintain confidentiality may subject you to federal and state penalties. If you are not the intended recipient, please immediately notify us by return email, and delete this message from your computer.
