Re: [PyMOL] Thermal ellipsoid plot
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 :
> 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 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 :
> > 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. ]
> >
> > 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 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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Re: [PyMOL] Thermal ellipsoid plot
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 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 :
> 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. ]
>
> 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 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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Re: [PyMOL] Thermal ellipsoid plot
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 :
> 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. ]
>
> 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 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.
>
>
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Re: [PyMOL] Thermal ellipsoid plot
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. ]
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 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.
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[PyMOL] Thermal ellipsoid plot
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
