PyRx - saving docked structure

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PyRx - saving docked structure

Postby bioman » Mon Mar 30, 2015 6:23 am

Hello,

I want to view docked structure in third party tools like pymol. How to save the docked structure?. I know the we can save docked structure in sdf format in analyse result tab. But when I open the sdf file in chimera, it shows only ligand structure and not the docked structure. Please help me
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Re: PyRx - saving docked structure

Postby sargis » Tue Mar 31, 2015 1:40 am

bioman wrote:I want to view docked structure in third party tools like pymol. How to save the docked structure?. I know the we can save docked structure in sdf format in analyse result tab. But when I open the sdf file in chimera, it shows only ligand structure and not the docked structure. Please help me

Hello,

Thank you for this feature request. This will be available in the upcoming 0.9.3 release of PyRx - http://sourceforge.net/p/pyrx/wiki/Changelog/
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Re: PyRx - saving docked structure

Postby bioman » Tue Mar 31, 2015 1:51 am

Thank you for reply. with the current version of PyRx, I think I can open in pymol with protein.pdbqt and ligand.pdbqt from PyRx workspace from the path we set in (edit-> preferences) to view the docked structure. Is that right?

HOw to do reverse virtual screening in PyRx?. I have many protein targets (approx around 50) and only one ligand. Is that possible in PyRx?
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Re: PyRx - saving docked structure

Postby sargis » Tue Mar 31, 2015 4:00 am

bioman wrote:Thank you for reply. with the current version of PyRx, I think I can open in pymol with protein.pdbqt and ligand.pdbqt from PyRx workspace from the path we set in (edit-> preferences) to view the docked structure. Is that right?

You are welcome. You can open protein.pdbqt and saved docked structure in sdf format from analyze result tab, or _out.pdqt or .dlg depending if you used Vina or AutoDock.

bioman wrote:HOw to do reverse virtual screening in PyRx?. I have many protein targets (approx around 50) and only one ligand. Is that possible in PyRx?

I don't know an easy way of doing this with the current version of PyRx, except running 50 separate dockings. I'll think about this for the next version of PyRx.
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