Amino Acids residues naming

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Amino Acids residues naming

Postby RaduT » Thu May 26, 2011 8:17 pm

Hello Sargis,

I'm curious if PyRx has a function for Amino Acids residues naming - after docking.
I need to have snapshots with the complex between ligand(s) and target... and it is possible to see the name of ligand (actually the name of file) and the names of bonded Amino Acids residues (if I failed to be coherent, please see the image bellow :? )?
Image

Regards, Radu.
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Re: Amino Acids residues naming

Postby sargis » Thu May 26, 2011 9:00 pm

Hello Radu,

Thank you for the message. It has not been implemented in PyRx yet. Could you please summit a New Ticket to make sure that this is included in one of the future releases. Copy/paste the original message should work there.

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Re: Amino Acids residues naming

Postby RaduT » Fri May 27, 2011 5:05 am

Thank you very much Sargis!

I just posted a ticket: https://sourceforge.net/apps/trac/pyrx/ticket/5

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Re: Amino Acids residues naming

Postby RaduT » Tue Jul 14, 2015 11:51 am

Hello again,

I'm using now the last version of software for Windows (PyRx-0.9.2, last updated on 28/04/2015). So, there is any implementation to see the names of amino acids residues involved in realization of H-bonds... or any alternative solution to actually see which amino acids residues are involved in formation of the complex?

Best regards, RaduT
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Re: Amino Acids residues naming

Postby sargis » Wed Jul 15, 2015 1:46 am

Hello Radu,

Thank you very much for using the last version of PyRx. Sorry I've been busy with other things that I forget about this.

With PyRx-0.9.2 you can display H-bonds between the ligand and the target by clicking on the greenish H icon on the toolbar or right-click on a molecule and select Display > Hydrogen Bonds as shown in the PyRx 0.9 Release Announcement. You can them mouse over the residue involved in formation of the complex and click on the "p" key on the keyboard. This will show the name of residue that you clicked. See https://youtu.be/9Zhce9-zcyo?t=5m3s for the video that shows this picking command.

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