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/
