> > > • Alignment of one-letter atom name such as C starts at column 14, while > > two-letter atom name such as FE starts at column 13. > > indicating a rule does exist.
There are programs that don't read/write the element from columns 77-78, so this rule still matters, but using it is less reliable, as Robbie wrote. After I wrote a function that reads pdb files for gemmi, over the next few years I received feedback about cases in which the element columns are absent and the element determined from the atom name is incorrect. The problem is primarily with 4-character atom names that can't be aligned, because they use all the four columns anyway. I added such comments to the code [1] when trying to get it right: // Atom names HXXX are ambiguous, but Hg, He, Hf, Ho and Hs (almost) // never have 4-character names, so H is assumed. // Similarly Deuterium (DXXX), but here alternatives are Dy, Db and Ds. // Only Dysprosium is present in the PDB - in a single entry as of 2022. // Old versions of the PDB format had hydrogen names such as "1HB ". // Some MD files use similar names for other elements ("1C4A" -> C). // ... or it can be "C210" [1] https://github.com/project-gemmi/gemmi/blob/148f37b7c6561c55553a255a6a4dd75d6bae888e/include/gemmi/pdb.hpp#L302 ######################################################################## To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1 This message was issued to members of www.jiscmail.ac.uk/CCP4BB, a mailing list hosted by www.jiscmail.ac.uk, terms & conditions are available at https://www.jiscmail.ac.uk/policyandsecurity/