'CA' for carbon-alpha is a 2-letter atom name so applying the rule exactly as stated it should start in column 13; it states that only 1-letter atom names (C, N, O) go in column 14. This must be a case of poorly-written documentation; it must mean 'element symbol' not 'atom name' in those cases where the 'atom name' begins with the 'element symbol', though as Robbie points out there's no rule that the atom name must begin with the element symbol.
COLUMNS DATA TYPE FIELD DEFINITION 13 - 16 Atom name Atom name. 77 - 78 LString(2) element Element symbol, right-justified. - 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. I. On Wed, May 15, 2024 at 11:56 AM Harry Powell < 0000193323b1e616-dmarc-requ...@jiscmail.ac.uk> wrote: > Sorry - just read that > > > • 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. > > Harry > > > On 15 May 2024, at 11:54, Harry Powell < > 0000193323b1e616-dmarc-requ...@jiscmail.ac.uk> wrote: > > > > Hi Ezra > > > > Thanks for this. > > > > In other words, would it be true to say that there are no actual rules > about what appears in columns 13-16 because “it's a rose by any other name”? > > > > Harry > > > >> On 15 May 2024, at 11:38, Ezra Peisach <ezra.peis...@rcsb.org> wrote: > >> > >> If you take a look at > https://www.wwpdb.org/documentation/file-format-content/format33/sect9.html#ATOM > >> > >> you will see the following: > >> > >> 77 - 78 LString(2) element Element symbol, > right-justified. > >> > >> Going by atom name will get you in trouble. As you stated calcium vs > Calpha. The element symbol comes from the chemical component dictionary. > >> > >> > >> Ezra > >> > >> > >> > >> On 5/15/24 6:28 AM, Harry Powell wrote: > >>> Hi folks > >>> > >>> I’m sure that this has been answered many times before (I’m sure that > when I was young I even read it here…), and I *know* that we should all be > using mmCIF, but I’m using PDB format files generated by a popular Python > module and I wanted to check the output against a definitive format > definition (if that’s not tautology). > >>> > >>> I noticed this because I was encouraged to try Moorhen and found that > a HEM (apparently written by this module) did not have the atoms connected > with bonds in the display. > >>> > >>> I’m particularly interested in metal atoms here, and want to be 100% > sure that I’ve found a calcium, say, and not a C-alpha. > >>> > >>> Q: Is it necessary to check columns 77-78 if I really want to be sure? > >>> > >>> I’ve read the following, but can’t see anything obvious in “official” > PDB documentation that what it says here is actually defined anywhere: > >>> > >>>> Atom names are composed of an atomic (element) symbol right-justified > in columns 13-14, and trailing identifying characters left-justified in > columns 15-16. A single-character element symbol should not appear in > column 13 unless the atom name has four characters (for example, see > Hydrogen Atoms). Many programs simply left-justify all atom names starting > in column 13. The difference can be seen clearly in a short segment of > hemoglobin (entry 3hhb): > >>>> > >>>> Correct: > >>>> HETATM 1071 FE HEM A 1 8.128 7.371 -15.022 24.00 16.74 > FE > >>>> HETATM 1072 CHA HEM A 1 8.617 7.879 -18.361 6.00 17.74 > C > >>>> HETATM 1073 CHB HEM A 1 10.356 10.005 -14.319 6.00 18.92 > C > >>>> HETATM 1074 CHC HEM A 1 8.307 6.456 -11.669 6.00 11.00 > C > >>>> HETATM 1075 CHD HEM A 1 6.928 4.145 -15.725 6.00 13.25 > C > >>>> > >>>> Incorrect: > >>>> HETATM 1071 FE HEM A 1 8.128 7.371 -15.022 24.00 16.74 > FE > >>>> HETATM 1072 CHA HEM A 1 8.617 7.879 -18.361 6.00 17.74 > C > >>>> HETATM 1073 CHB HEM A 1 10.356 10.005 -14.319 6.00 18.92 > C > >>>> HETATM 1074 CHC HEM A 1 8.307 6.456 -11.669 6.00 11.00 > C > >>>> HETATM 1075 CHD HEM A 1 6.928 4.145 -15.725 6.00 13.25 > C > >>> I’m sure that someone here will say “why don’t you look at *****, it’s > obvious”, in which case - many thanks! > >>> > >>> help > >>> > >>> Harry > >>> > >>> > ######################################################################## > >>> > >>> 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/ > > > > ######################################################################## > > > > 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/ > > ######################################################################## > > 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/ > ######################################################################## 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/
