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/
