Re: [PyMOL] get_area algorithm and dot_density accuracy

Hi I am not sure which method is being used by PyMOL but because the algorithm uses a dot density term it is likely the Shrake & Rupley algorithm also known as the rolling ball method. You should read the FreeSASA article (freely available https://f1000research.com/articles/5-189/v1 ). The author

Re: [PyMOL] get_area algorithm and dot_density accuracy

Thank you for your reply. With regard to the algorithm used, do you have any idea which algorithm is used in the Pymol calculations? DSSP is likely to be using the rolling ball method. Regards. On Thu, Apr 27, 2017 at 1:35 PM, Emilio Xavier Esposito wrote: > Hi > The

Re: [PyMOL] get_area algorithm and dot_density accuracy

Hi The accuracy of the calculation depends on the dot_density value (the amount of sampling done) with 1 being the lowest quality and 4 being the best quality. A dot_density value of 1 uses less computational resources (time) than a dot_density of 4 because of the amount of sampling performed to

Re: [PyMOL] get_area algorithm and dot_density accuracy

I would appreciate any help regarding this. On Tue, Apr 25, 2017 at 12:36 PM, Ahmad Abdelzaher wrote: > Hello, > > Does the get_area command use the rolling ball algorithm? Which > dot_density corresponds to the best accuracy 1 or 4? Is there a reason > why it consumes