When I've wanted to show an internal cavity I've found the best route is: pdb file->voidoo->mapman->ccp4 map->pymol
(play with your probe size in voidoo to prevent thr probe from "rolling out" of your cavity) You can load the ccp4 formatted cavity maps into xfit/coot, you get your volume measurements and draw a nice picture (you cavity is now an "object" in pymol, and you have a little more flexibility as to how it is rendered). The different surfacing algorithms between programs behave differently, I always get weird face normals when trying to use pymol surface for internal cavities. A lab I used to be in had a copy on insightII which seemed to do a better job with those... -----Original Message----- From: CCP4 bulletin board on behalf of Green, Todd Sent: Mon 3/12/2007 8:04 AM To: CCP4BB@JISCMAIL.AC.UK Subject: [ccp4bb] surface drawings Hello All, I would like to make an illustration which has a semi-transparent surface rendering for a large cavity. I just want the suface to cover the cavity not the entire protein (which will most likely exist as a ribbon drawing). Is there a way to set a boundary for a surface drawing? By that, I mean pick a point within the cavity and set a radius to draw a solvent accessible surface and thusly only those points falling within the radius are shown. Seems simple enough, but I haven't quite figured it out as of yet. Thanks in advance for any advise. Todd
