Miguel wrote:
this mostly addresses nucleotidic HET groups (large HET)Do you have any recommendations as to how we can address this problem?
http://www.rcsb.org/pdb/docs/format/pdbguide2.2/part_62.html
' - In large het groups it sometimes is not possible to follow the
convention ...'
so if there is a
select hetero and nucleic
the N,A,B which confused element detection (and are part of all atom
names) must be striped off.
Two critical phrases in this page are:
"The element symbol is always present on each ATOM record"
and
"For example, a hydrogen named HG11 in columns 13 - 16 is differentiated from a mercury atom by the element symbol in columns 77 - 78."
and element composition is mentioned in FORMUL record!
http://www.rcsb.org/pdb/docs/format/pdbguide2.2/part_41.html
I did not understand this page.
with 3dfr http://www.imb-jena.de/cgi-bin/SCOPlnk.exe?JMOL=3DFR the FORMUL record looks like this
FTNOTE 2 SEE REMARK 7. 3DFR 119 HET NDP 1 48 NADPH 3DFR 120 HET MTX 2 33 METHOTREXATE 3DFR 121 FORMUL 2 NDP C21 H27 N7 O17 P3 3DFR 122 FORMUL 3 MTX C20 H22 N8 O5 3DFR 123 FORMUL 4 HOH *264(H2 O1) 3DFR 124 HELIX 1 HB LEU 23 THR 34 1 3DFR 125
therefore there are only C, H, N, O, P atoms possible in the HETERO group NDP (21 * C, 27 * H, 7* N, 17 * O, 3* P if all are resolved in the PDB file)
therefore
NC4* is not Nc but may be a C
NO4* is not No but may be an O
NP is not Np but may be a P
NN1 is not Nn but may be a N
Regards, Jan
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