[PyMOL] Sausage representation

Hello, I found in this repository http://muralab.org/~cmura/PyMOL/ an script (average3d.py) to perform the sausage representation in PyMOL. Although it works perfectly good with the pdbs given in the examples, I couldn't get the same results for my molecule. After performing all the RMSD

Re: [PyMOL] Sausage representation

Hi Daniel, Apparently, no b-factors were assigned, or the CA positions in all states are identical. Here is a similar script, maybe that works better for you (uses “rmsf2b” from PSICO): run https://raw.githubusercontent.com/speleo3/pymol-psico/master/psico/editing.py fetch 1nmr, async=0

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

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 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