While converting the attached file of POPE lipid, which has three hydrogens with four-letter names on an amine group the conversion to svg produces a wrong result.
After the conversion the svg file should have three explicit hydrogens on the nitrogen atoms, however, babel produces a NH2 group and three scattered Xx atoms.
The issue is resolved if the four-letter atom names on nitrogen are changed to three-letter names in the pdb. Four-leter hydrogens on other atoms and non-hydrogen four-letter atoms do not have this issue.
System info:
Open Babel 2.3.2 -- Dec 19 2014 -- 19:23:22 from Macports
Darwin bond 14.4.0 Darwin Kernel Version 14.4.0: Thu May 28 11:35:04 PDT 2015; root:xnu-2782.30.5~1/RELEASE_X86_64 x86_64