Download your LIT When the conversion process is complete, you can download the LIT file. Convert PDF to LIT Click Convert button to start conversion. Upload PDF-file Click Choose File button to select a pdf file on your computer. (PyMol is one such program.Convert Lit To Pdb By waltitalchamp1975 Follow | Public To generate those atoms, use a program which can use the PDB symmetry records to generate the symmetric partners. I'm guessing the atoms you're missing are related by crystallographic symmetry to the ones that are present. (CRYST1, SCALE1, SCALE2 and SCALE3 records). Regarding the "missing atoms", the PDB file contains a crystallographic symmetry record in the first four lines. VMD doesn't seem to help (it reads things fine, but doesn't add the element annotation), but PyMol is able to read in the file and when re-saving the molecule will put the correct values in columns 77-78. If you don't want to manually edit the lines, you just need to pass the PDB file through a program that can make sense of the AU atoms, and will output the element name in the appropriate colum. But for C/N/O it's okay, as Open Babel is able to figure out the element from the atom name. If you manually edit the ATOM lines to contain the letters "Au" in columns 77-78, then Open Babel is able to make the conversion, but still warns about the C/N/O atoms which don't have their elements correctly designated. Your PDB contains gold atoms, and Open Babel doesn't know how to handle the "AU" atoms. That's what's causing Open Babel to choke.
Parsing this is tricky, though, as it doesn't always work. Older PDBs (and lazy PDB-outputting software) don't do that.įor the most part that works, as the atom name entry normally contains the element designation. Basically, the official PDB specification requires that the atom names be present off to the right-hand side of each ATOM/HETATM line. This thread from the OpenBabel mailing list goes into more details. Problems reading a HETATM or ATOM record.Ĭolumns 77-78 should contain the element symbol of an atom.
*** Open Babel Warning in parseAtomRecord If you take a look at the output, you see a bunch of the following warnings. The conversion issue you're seeing is because the PDB you're using is not technically well-formatted.
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