mittinatten
commented
5 years ago Not sure if I can help you, not a Pymol expert, but if you post the pdb here, I can maybe tell where the problem lies. On Thu, 4 Oct 2018 at 19:33, Cheng Fang notifications@github.com wrote:
Hi,
I was trying to use this tool to calculate the SASA for a 3D small molecule, especially for some specific atoms in the molecule. I saved the molecule into pdb file with Pymol, and loaded using freesasa python API.
import freesasa structure = freesasa.Structure("1.pdb") I got the error: FreeSASA:lib\src\structure.c:679: error: input had no valid ATOM or HETATM lines FreeSASA:lib\src\structure.c:686: error: Traceback (most recent call last): File "", line 1, in File "freesasa.pyx", line 457, in freesasa.Structure.init Exception: Error reading '1.pdb'.
Would you mind help me figure out how to generate valid PDB file of a given 3D small molecule for this program?
Thank you!
Cheng
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Hi,
I was trying to use this tool to calculate the SASA for a 3D small molecule, especially for some specific atoms in the molecule. I saved the molecule into pdb file with Pymol, and loaded using freesasa python API.
Would you mind help me figure out how to generate valid PDB file of a given 3D small molecule for this program?
Thank you!
Cheng