I'd like to create a surface for the entire chain A and then limit its display by proximity to chain E but without calculating the whole surface. This doesnâ

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: Molecule" this is not equal to e.g., "Context: Chain" (which is not an option) and thus produces the undesired result.

If you try the same on a structure with no gaps, e.g., 1afo, where chain=molecule, 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 molecule 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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