Chimera calls the MMTK Python API directly and does not generate any separate MMTK Python scripts. This is because there are a number of steps that Chimera needs to perform before MMTK can be used, eg adding hydrogens, assigning charges, etc. The main source code is in class MMTKinter in file CHIMERA/share/MMMD/MMTKinter.py. As for using MMTK outside of Chimera, you can certainly save the minimized structure as input for MMTK. The partial charges, however, may be a bit tricky. I've not used MMTK outside the context of Chimera so I'm not that familiar with all the different options available. Probably, the easiest way to get a usable MMTK configuration externally is to modify MMTKinter.py so to add an interface for calling MMTK.save() to save the Chimera-created universe to a file, and then use MMTK.load() in your script to read it back in. Conrad Jean Didier Pie Marechal wrote:
Hi everyone,
I have a question regarding the MMTK interfase. How complicate it is to get the hand on a the MMTK script and input files generated by chimera to perform the minimization ? Is it located in some subfolder? Is there a way to write it down so that I can perform further calculations outside the chimera environment? All the best, JD
Dr. Jean-Didier Maréchal Lecturer Computational Bioorganic and Bioionorganic Chemistry @ Transmet Unitat de Química Física Departament de Química Universitat Autònoma de Barcelona Edifici C.n. 08193 Cerdanyola (Barcelona) Tel: +34.935814936 e-mail: JeanDidier.Marechal@uab.es