Hi all, I tried making a 2d picture of PDB 2MAL (-i pdb). After several failed attempts I tried converting to a smiles string and got a useful message: molecule too large, 1200+ atoms, openbabel is limited to 1000.
Could this error be thrown by other converters? -- I tried -o svg, -o png, and -o sdf, and in each case obabel/obgui pegged one cpu core at 100% and sat there -- the longest I tried before killing it was 20 minutes as reported by top. (The other question is whether there's a way/any plans to relax the limit: we're mostly dealing with macromolecules averaging ~1,500 atoms here.) 8-core/16GB RAM, linux centos 6.3 x86_64, openbabel 2.3.2 built from source. Thx -- Dimitri Maziuk Programmer/sysadmin BioMagResBank, UW-Madison -- http://www.bmrb.wisc.edu
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