Mr. Thomas Holder, Many thanks for your help. I can manage it.
Best regards, Koji 2019年6月26日(水) 18:56 Thomas Holder <thomas.hol...@schrodinger.com>: > Hi Koji, > > Yes it is my understanding that sphere_scale 1.1932 would correspond to > 30% probability. > > Cheers, > Thomas > > > On Jun 25, 2019, at 12:26 PM, koji naka <pasuvn...@gmail.com> wrote: > > > > Dear Mr. Thomas Holder, > > > > Thank you very much for your kind reply. > > I am very happy to know the scale factor for the 50% probability, but I > don't understand well. > > From the table, can I take a value the scale? For example, in case of > 30% probability, is it ok to set " set sphere_scale, 1.1932"? or not? > > > > I am sorry for bothering you again. > > > > Best regards, > > Koji > > > > 2019年6月25日(火) 18:49 Thomas Holder <thomas.hol...@schrodinger.com>: > > 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. > > > > -- > Thomas Holder > PyMOL Principal Developer > Schrödinger, Inc. > >
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