On Apr 12, 2010, at 5:05 AM, Guy Nimrod wrote:

Hello, When I load complex structure (e.g., pdb 3mht) and show the surface of one chain (e.g. selectchainA; action->surface->show), the generated surface does not cover the interface between the query protein and the other chains. Consequently, the interface appears as a hole in the surface (see attached figure). Is there an easy way to visualize the whole surface (i.e. the generated surface on a selected chain will disregard chains which are not selected)?

Hi Guy, When you surface some subset of atoms in Chimera, Chimera still considers all atoms in the same "surface category" as the subset for purposes of computing the surface -- it just doesn't show the surface of the atoms not in the subset. So for example if you ask for a surface on a single residue Chimera doesn't make a surface that completely encloses the residue -- the surface is "open" where the residue connects to the rest of the molecule. Similarly, a single chain of a multi-chain molecule may not be completely enclosed if Chimera considers other chains of the molecule to be in the same surface category. That is what has happened here. Chain A (the protein) and the chains C and D (the nucleic acid) have been classified into the same surface category (main). To get the enclosed surface that you want you need to put chain A into a surface category of its own and surface that. These two commands will accomplish that: surfcat prot :.a surf prot The surface actually inter-penetrates the nucleic acid because of the flipped-out base, like this: --Eric Eric Pettersen UCSF Computer Graphics Lab http://www.cgl.ucsf.edu