[PyMOL] real time minization in Pymol

2015-11-23 Thread Albert 
Hello:

I just found a a very nice module of pymol, called "Molecular 
Sculpting". However, according to the description in Pymolwiki, it works 
like a real-time energy minimizer, except that it isn't minimizing the 
energy. Instead, its just trying to return local atomic geometries 
(bonds, angles, chirality, planarity) to the configuration the molecules 
possess when they were first loaded into PyMOL.

So I am just wondering does the developer have any planning to improve 
this nice too? For instance introducing forcefiled for this tool (eg: 
Amber FF for protein, GAFF for the ligand). There is a "optimize" plugin 
in Pymol, maybe the developer can consider merge them together?

Thank you very much

Albert

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Re: [PyMOL] real time minization in Pymol

2015-11-23 Thread Albert 
Yes, I also really love this function. However, for the sake of 
accuracy, I believe many users will also strongly demand for introducing 
forcefield for minimization..I am looking forward to see that 
"optimize" plugin would somehow merged into "Molecular Sculpting".At 
least, it is very easy and free to get access to Amber and GAFF forcefield.

Thanks again.

On 11/23/2015 05:07 PM, H. Adam Steinberg wrote:
> I would love to see this feature improved!
>
> Try it out if you have never used it. It works quite well. It is quite 
> processor intensive and it can take over your computer when it is running…. I 
> have also found when you uncheck it in the menu, it will still continue to 
> run and I end up force quitting to get it to stop.


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Re: [PyMOL] real time minization in Pymol

2015-11-23 Thread H. Adam Steinberg 
I would love to see this feature improved!

Try it out if you have never used it. It works quite well. It is quite 
processor intensive and it can take over your computer when it is running…. I 
have also found when you uncheck it in the menu, it will still continue to run 
and I end up force quitting to get it to stop.

> On Nov 23, 2015, at 8:46 AM, Albert  wrote:
> 
> Hello:
> 
> I just found a a very nice module of pymol, called "Molecular 
> Sculpting". However, according to the description in Pymolwiki, it works 
> like a real-time energy minimizer, except that it isn't minimizing the 
> energy. Instead, its just trying to return local atomic geometries 
> (bonds, angles, chirality, planarity) to the configuration the molecules 
> possess when they were first loaded into PyMOL.
> 
> So I am just wondering does the developer have any planning to improve 
> this nice too? For instance introducing forcefiled for this tool (eg: 
> Amber FF for protein, GAFF for the ligand). There is a "optimize" plugin 
> in Pymol, maybe the developer can consider merge them together?
> 
> Thank you very much
> 
> Albert
> 
> --
> Go from Idea to Many App Stores Faster with Intel(R) XDK
> Give your users amazing mobile app experiences with Intel(R) XDK.
> Use one codebase in this all-in-one HTML5 development environment.
> Design, debug & build mobile apps & 2D/3D high-impact games for multiple OSs.
> http://pubads.g.doubleclick.net/gampad/clk?id=254741551=/4140
> ___
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H. Adam Steinberg
7904 Bowman Rd
Lodi, WI 53555
608/592-2366


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