I think it is a pdb rule. Here are some of the rules: http://www.wwpdb.org/documentation/format33/sect9.html
Charges (confusingly) could be 2+ etc. Regards Garib On 4 Oct 2011, at 16:41, Eleanor Dodson wrote: > OK > > So the ATOM TYPE has ZN O C S etc in column 77/78 and the +2 etc in 79/80 > > Is there any documentation for this? > > E > > > > On 10/04/2011 03:56 PM, Garib N Murshudov wrote: >> If you will put element names in correct positions then refmac may have a >> chance to find it. Here is corrected positions: >> >> ATOM 1893 O HOH A 258 -8.934 52.268 49.467 0.00 66.53 >> O >> ATOM 1894 ZN ZN B 1 -10.456 38.580 26.267 1.00 57.36 >> ZN+2 >> ATOM 1895 O HOH C 1 -5.932 42.917 25.589 1.00 24.02 >> O >> >> In your case all element names are moved towards left and B value of ZN is >> in incorrect position also. >> >> ATOM 1893 O UNK A 258 -8.934 52.268 49.467 0.00 66.53 O >> ATOM 1894 ZN+2 ZN B 1 -10.456 38.580 26.267 1.00 57.36 ZN+2 >> ATOM 1895 O HOH C 1 -5.932 42.917 25.589 1.00 24.02 O >> >> Regards >> Garib >> >> >> On 4 Oct 2011, at 15:31, Eleanor Dodson wrote: >> >>> Can anyone advise me how to get the Zn+2 formfactor from atomsf.lib >>> >>> The input coordinate is given atom type ZN+2 but the formfactor is that for >>> Zn: >>> I changed the atom name to Zn+2 but that made no difference... >>> >>> ATOM 1893 O UNK A 258 -8.934 52.268 49.467 0.00 66.53 O >>> ATOM 1894 ZN+2 ZN B 1 -10.456 38.580 26.267 1.00 57.36 ZN+2 >>> ATOM 1895 O HOH C 1 -5.932 42.917 25.589 1.00 24.02 O >>> >>> refmac log says: >>> >>> loop_ >>> _atom_type_symbol >>> _atom_type_scat_Cromer_Mann_a1 >>> _atom_type_scat_Cromer_Mann_b1 >>> _atom_type_scat_Cromer_Mann_a2 >>> _atom_type_scat_Cromer_Mann_b2 >>> _atom_type_scat_Cromer_Mann_a3 >>> _atom_type_scat_Cromer_Mann_b3 >>> _atom_type_scat_Cromer_Mann_a4 >>> _atom_type_scat_Cromer_Mann_b4 >>> _atom_type_scat_Cromer_Mann_c >>> >>> >>> N 12.2126 0.0057 3.1322 9.8933 2.0125 28.9975 1.1663 >>> 0.5826 -11.5290 >>> C 2.3100 20.8439 1.0200 10.2075 1.5886 0.5687 0.8650 >>> 51.6512 0.2156 >>> O 3.0485 13.2771 2.2868 5.7011 1.5463 0.3239 0.8670 >>> 32.9089 0.2508 >>> SE 17.0006 2.4098 5.8196 0.2726 3.9731 15.2372 4.3543 >>> 43.8163 2.8409 >>> S 6.9053 1.4679 5.2034 22.2151 1.4379 0.2536 1.5863 >>> 56.1720 0.8669 >>> ZN 14.0743 3.2655 7.0318 0.2333 5.1625 10.3163 2.4100 >>> 58.7097 1.3041 >>> >>> >>> Eleanor >> >> Garib N Murshudov >> Structural Studies Division >> MRC Laboratory of Molecular Biology >> Hills Road >> Cambridge >> CB2 0QH UK >> Email: ga...@mrc-lmb.cam.ac.uk >> Web http://www.mrc-lmb.cam.ac.uk >> >> >> >> Garib N Murshudov Structural Studies Division MRC Laboratory of Molecular Biology Hills Road Cambridge CB2 0QH UK Email: ga...@mrc-lmb.cam.ac.uk Web http://www.mrc-lmb.cam.ac.uk
