Figure 6. PDB structure 104l. (a) Surface representation of the two chains together. (b) Surface representation of the two chains sepa- rately. The two representations diﬀer in the interface between the two chains. Nucleic Acids Research, 2009, Vol. 37, Web Server issue W569 are found as similar by the comparison are colored with a gradient from Nter to Cter (Figure 5). Below the two structures are the residues of the two sequences and the residues of each sequence that belong to the solution have the same color as in the Jmol visualization. The results of the multiple pairwise surface comparison are summarized in a table sorted by number of corre- sponding atoms for each pair. Each structure in the left- hand column is linked with the page that stores the results of the comparison between that structure and the query structure. A note on chain selection Users have to keep in mind a caveat when dealing with chain selection for a structure with multiple chains. That is, the surface representation of two contiguous chains is diﬀerent from the surface representation of each of the two chains separately (Figure 6), and therefore the result of the comparison can be diﬀerent. For example, the molecular surface of 1atp, chain E, is diﬀerent from the molecular surface of 1atp, chains E and I. In fact, the ATP binding pocket of 1atp,E is an open cavity, while the ATP binding pocket of 1atp,EI is an internal cavity. Hence, the two surfaces are diﬀerent and the optimal alignment between the ATP binding pockets of 1atp,EI (both chains) and of 1csn,A is slightly diﬀerent from the optimal alignment between the ATP binding pockets of 1atp,E (only one chain) and of 1csn,A (Figure 7). In this example, the solution of the comparison between 1atp,EI and 1csn,A contains only corresponding atoms from chain E on structure 1atp. The web server gives a warning mes- sage, telling the user that the alignment may change if run again on a single chain (in this case chain E) of a multiple chain protein. PERFORMANCE MolLoc web server uses several diﬀerent software mod- ules to build the surface representation, ﬁnd the binding sites and the cavities, and to compare the surfaces. Figure 7. 1atp in purple, 1csn in blue. (a) The result of the comparison between 1atp,E and 1csn,A. (b) The result of the comparison of both chains of 1atp (E and I) with 1csn,A. In this case, diﬀerences in the initial surface lead to diﬀerences in the surface alignment.