Re: [PyMOL] New plugin: PyMOLProbity

[Maheshwaran.V]

Wonderful work Jared...



On Jan 18, 2017 3:58 AM, "Thomas Holder" 
wrote:

> Great work Jared!
>
> Cheers,
>   Thomas
>
> On 17 Jan 2017, at 20:02, Albert  wrote:
>
> > fantastic job!!
> >
> > Thanks a lot.
> >
> > Albert
> > On 01/16/2017 10:16 PM, Sampson, Jared M. wrote:
> >> Dear PyMOL Users,
> >>
> >> I am pleased to introduce a new plugin called PyMOLProbity which allows
> a PyMOL user to visualize MolProbity-style structural validation data
> directly in a PyMOL session. The programs Reduce, Flipkin, and Probe from
> the well-known MolProbity software package allow generation of data in
> "kinemage" (kinetic image) format to illustrate atom-atom contacts (dots)
> and clashes (spikes), and the new plugin now makes it possible to utilize
> the same programs to produce similar results in PyMOL scenes.
> >>
> >> I have put together a page on the PyMOL Wiki with a brief summary of
> its features and basic how-to information.  (Please note that the
> MolProbity executables are only available for Linux/MacOS, so PyMOLProbity
> isn't yet useful on Windows.)
> >>
> >> My work on this plugin was supported by the Warren L. DeLano Memorial
> PyMOL Open-Source Fellowship.  I would like once again to thank Schrödinger
> for the opportunity to work on this project, and in particular would like
> to thank the PyMOL developers for their support and feedback along the way.
> >>
> >> I hope many of you will find it useful.  If you come across any bugs or
> have any feature requests or other suggestions, please feel free to email
> me directly or create a new issue on Github.
> >>
> >> Happy PyMOLing!
> >>
> >> Cheers,
> >> Jared
>
> --
> Thomas Holder
> PyMOL Principal Developer
> Schrödinger, Inc.
>
>
> 
> --
> Check out the vibrant tech community on one of the world's most
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Re: [PyMOL] New plugin: PyMOLProbity

[Thomas Holder]

Great work Jared!

Cheers,
  Thomas

On 17 Jan 2017, at 20:02, Albert  wrote:

> fantastic job!!
> 
> Thanks a lot.
> 
> Albert
> On 01/16/2017 10:16 PM, Sampson, Jared M. wrote:
>> Dear PyMOL Users, 
>> 
>> I am pleased to introduce a new plugin called PyMOLProbity which allows a 
>> PyMOL user to visualize MolProbity-style structural validation data directly 
>> in a PyMOL session. The programs Reduce, Flipkin, and Probe from the 
>> well-known MolProbity software package allow generation of data in 
>> "kinemage" (kinetic image) format to illustrate atom-atom contacts (dots) 
>> and clashes (spikes), and the new plugin now makes it possible to utilize 
>> the same programs to produce similar results in PyMOL scenes.
>> 
>> I have put together a page on the PyMOL Wiki with a brief summary of its 
>> features and basic how-to information.  (Please note that the MolProbity 
>> executables are only available for Linux/MacOS, so PyMOLProbity isn't yet 
>> useful on Windows.)
>> 
>> My work on this plugin was supported by the Warren L. DeLano Memorial PyMOL 
>> Open-Source Fellowship.  I would like once again to thank Schrödinger for 
>> the opportunity to work on this project, and in particular would like to 
>> thank the PyMOL developers for their support and feedback along the way.
>> 
>> I hope many of you will find it useful.  If you come across any bugs or have 
>> any feature requests or other suggestions, please feel free to email me 
>> directly or create a new issue on Github.
>> 
>> Happy PyMOLing!
>> 
>> Cheers,
>> Jared

-- 
Thomas Holder
PyMOL Principal Developer
Schrödinger, Inc.


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Re: [PyMOL] New plugin: PyMOLProbity

[Albert]

fantastic job!!

Thanks a lot.

Albert

On 01/16/2017 10:16 PM, Sampson, Jared M. wrote:

Dear PyMOL Users,

I am pleased to introduce a new plugin called PyMOLProbity 
 which allows a PyMOL 
user to visualize MolProbity-style structural validation data directly 
in a PyMOL session. The programs Reduce, Flipkin, and Probe from the 
well-known MolProbity  software 
package allow generation of data in "kinemage" (kinetic image) format 
to illustrate atom-atom contacts (dots) and clashes (spikes), and the 
new plugin now makes it possible to utilize the same programs to 
produce similar results in PyMOL scenes.


I have put together a page on the PyMOL Wiki 
 with a brief summary of 
its features and basic how-to information.  (Please note that the 
MolProbity executables are only available for Linux/MacOS, so 
PyMOLProbity isn't yet useful on Windows.)


My work on this plugin was supported by the Warren L. DeLano Memorial 
PyMOL Open-Source Fellowship.  I would like once again to thank 
Schrödinger for the opportunity to work on this project, and in 
particular would like to thank the PyMOL developers for their support 
and feedback along the way.


I hope many of you will find it useful.  If you come across any bugs 
or have any feature requests or other suggestions, please feel free to 
email me directly or create a new issue 
 on Github.


Happy PyMOLing!

Cheers,
Jared


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Re: [PyMOL] making a plane

[Tsjerk Wassenaar]

Hi Vitaly,

You have several options, but if the loops are nicely bent, the best is
probably doing PCA on the coordinate sets of the loops and calculate the
angle between the smallest eigenvectors.

Is that enough information? Do you insist on drawing the planes?

Cheers,

Tsjerk

On Jan 17, 2017 15:11, "chemocev marker"  wrote:

> Hi
> I am analyzing the dynamics of the loop and interested to define the loop
> as plane. Is there is a way in the pymol, if I can define the loop as plane
> and can measure the angle between these plane in different model??
>
> Best
> J. Vitali
>
> 
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[PyMOL] making a plane

[chemocev marker]

Hi
I am analyzing the dynamics of the loop and interested to define the loop
as plane. Is there is a way in the pymol, if I can define the loop as plane
and can measure the angle between these plane in different model??

Best
J. Vitali
--
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