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/
