Hi Koji, Interesting question, I wasn't aware of the ellipsoid_probability setting.
The probability to radius conversion is done with a lookup table, see: https://github.com/schrodinger/pymol-open-source/blob/d1359f125d/layer2/RepEllipsoid.cpp#L114 To get sphere scaling equivalent of ellipsoid_probability=0.5, you can do: set sphere_scale, 1.53820 I calculated this value with the following script: problevel = [ \ 0.4299, 0.5479, 0.6334, 0.7035, 0.7644, \ 0.8192, 0.8694, 0.9162, 0.9605, 1.0026, \ 1.0430, 1.0821, 1.1200, 1.1570, 1.1932, \ 1.2288, 1.2638, 1.2985, 1.3330, 1.3672, \ 1.4013, 1.4354, 1.4695, 1.5037, 1.5382, \ 1.5729, 1.6080, 1.6436, 1.6797, 1.7164, \ 1.7540, 1.7924, 1.8318, 1.8724, 1.9144, \ 1.9580, 2.0034, 2.0510, 2.1012, 2.1544, \ 2.2114, 2.2730, 2.3404, 2.4153, 2.5003, \ 2.5997, 2.7216, 2.8829, 3.1365, 6.0000 ] iprob = int((cmd.get_setting_float('ellipsoid_probability') + 0.01) * 50 - 1) pradius = problevel[iprob] cmd.set('sphere_scale', pradius * cmd.get_setting_float('ellipsoid_scale')) Hope this helps. Cheers, Thomas > On Jun 24, 2019, at 7:21 AM, koji naka <pasuvn...@gmail.com> wrote: > > Dear all, > > The size of isotropic atoms plotted by using "alter all, vdw = sqrt(b/8)/pi" > and "show sphere" looks small compared with the size of anisotropic atoms > displayed by "show ellipsoid" in PyMOL default setting with 50% probability. > > How can I plot the isotropic atoms with 50% probability? > > The data is a pdb file converted from a cif through Mercury software. > > Thank you very much for your help. > > Best regards, > Koji > > > _______________________________________________ > PyMOL-users mailing list > Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net > Unsubscribe: > https://sourceforge.net/projects/pymol/lists/pymol-users/unsubscribe -- Thomas Holder PyMOL Principal Developer Schrödinger, Inc. _______________________________________________ PyMOL-users mailing list Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net Unsubscribe: https://sourceforge.net/projects/pymol/lists/pymol-users/unsubscribe
