At http://jmol.sourceforge.net/jscolors/#Chains are shown 26 colors mapped to chain IDs A-Z, and the same colors to a-z. This appears to be correct.
There is stated "Atoms in HETERO groups (PDB files only) are colored darker than those in ATOM records." This appears to be correct for chains A-Q, which have light colors for ATOM and darker colors for HETATM. However, chains R-Z ATOM colors are dark, and the HETATM colors are shown as lighter. So I suggest that the above sentence be changed to: "Atoms in HETERO groups (PDB files only) are colored darker for chains A-Q (or lighter for chains R-Z) than those in ATOM records." There it is stated that chains with ID "none/numeric" are colored white. This is incorrect in Jmol 12.0.25. Chains 0-9 are colored (it appears to me) identically to chains P-Y. So I suggest: 1. Include chain ID's 0-9 in the tabular list grouped with P-Y respectively. 2. Change "none/numeric" in the last row of the table to "none". None (blank) is no longer legal in remediated PDB files, but may occur in PDB files downloaded before remediation, or in PDB files not obtained from the WWPDB. I suggest adding the following to the end of the paragraph of text above the table: "The PDB format requires that each chain ID be a non-blank alphanumeric character (http://www.wwpdb.org/documentation/format32/sect9.html#ATOM). Thus, a maximum of 26 times 2 (upper and lower case letters A-Z and a-z are permitted) plus 10 (chain IDs 0-9), or 62 chains is permitted in a single model within a PDB file. An example with 62 chains is 2zkr. PDB files obtained before remediation may have chain IDs that are blank or not alphanumeric (e.g. punctuation characters) but this is no longer permitted. Although chain A is the same color as chain a (and so forth), they may be selected independently (see "set chainCaseSensitive")." -Eric ------------------------------------------------------------------------------ Learn how Oracle Real Application Clusters (RAC) One Node allows customers to consolidate database storage, standardize their database environment, and, should the need arise, upgrade to a full multi-node Oracle RAC database without downtime or disruption http://p.sf.net/sfu/oracle-sfdevnl _______________________________________________ Jmol-users mailing list [email protected] https://lists.sourceforge.net/lists/listinfo/jmol-users
