On Apr 17, 2008, at 8:59 AM, Gareth Young wrote:
So I've been trying to make an 'inverted surface'. Basically I have a cavity inside a protein which is almost completely surrounded and so it is hard to illustrate it to others without removing parts of the protein (which I could of course do). Does Chimera have a function to mark the inside of a cavity with a surface, then allowing the user to remove the protein and just leave the surface so as to illustrate the size and shape of the cavity in relation to the protein.
Have I explained that clearly enough???
Hi Gareth, If this is a standard PDB you can fetch the structure from the CASTp database (File->Fetch By ID...) which will bring up an interface that will allow you to browse the pockets of the structure, with only the browsed pocket being surfaced. If you have a non-standard PDB, you will need to identify some residues near the pocket (let's say they were residues 15 to 19) and then use a command like: ~surf :15-19 z>5 to hide surfaces further than 5 angstroms from those residues, which should hide most of the "outside" surface. Then: ~disp will hide the structure. If you don't know the pocket residues, you might clip through the outside surface with the Side View clip planes and then use the mouse-hovering popup balloons to identify some residues. If your pocket has a channel to the outside, you might want to get a clean cut through the channel by using per-model clipping on the surface and orienting the clip plane so that it cuts the channel. The Per-Model Clipping tool is in the Depiction tools category. I'd like to get Chimera to handle CASTp results for non-standard PDBs, but haven't gotten to that yet. --Eric Eric Pettersen UCSF Computer Graphics Lab http://www.cgl.ucsf.edu