Article ID: 516 - Last Modified: September 19, 2013
I'd like to create the surface for the entire chain A and then limit its display by proximity to chain E but without calculating the whole surface. I tried the following expression with Context set to Molecule, but it doesn't seem to work:
(within 6 (chain.name E)) AND (chain.name A)
I get a surface in which the selected residues appear as though they are a full molecule. The back surface, which is in contact with other atoms of chain A, is generated as though there are no other atoms of chain A.
How do I achieve what I want?
The reason for this behavior is most likely due to the presence of gaps. Maestro would indicate that there are 5 molecules present in chain A (due to gaps), so when you create a surface with Context set to Molecule, this is not equivalent to setting the context to Chain (which is not an available option) and thus produces the undesired result.
If you try the same expression on a structure with no gaps, e.g., 1afo, where the chains are single molecules, then using a similar ASL string:
(within 6 (chain.name B)) AND (chain.name A)
generates the desired surface correctly, i.e., with no "back surface".
Since there is no Chain option for the context, one possibility would be to split the complex into separate entries by chain, and use Entry as the context when displaying both (or all) chains.
Keywords: surface generation , gaps, molecules, context:molecule
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