I am a beginner at PyMol software and currently, I am using TmoleX to do my optimization of molecules in the Hydro-formylation process. I need PyMol to calculate the RMSD value. How can I open a file from Turbomole (TmoleX) to PyMol and calculate the RMSD value? I need to calculate RMSD for the Crystal structure and the Optimized structure of mine.
You will have to export the coordinates in a file format that PyMOL can understand.
Search the appropriate TMolX Documentation (https://www.turbomole.org/turbomole/turbomole-documentation/) for "export", export the file in a format understood by PyMOL, then you can load the files into PyMOL
(https://pymolwiki.org/index.php/Load)
mol or mol2 will be preferable to pdb, because they also encode the information about bond order, which pdb normally does not
Since you are exporting your molecule from TMolX, I assume it is not a protein. Therefore the "align" command in PyMOL, which pairs atoms between two objects based on a sequence alignment and does a backbone alignment, will not be the appropriate tool to do it. Instead, you want to use pair-fit from the command line (https://pymolwiki.org/index.php/Pair_fit) or use the Pair-fitting wizard (Wizards menu)
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