Doubt about results in Pyrx 0.9.2 version

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Doubt about results in Pyrx 0.9.2 version

Postby oivalf_nix » Mon May 26, 2014 3:00 pm

Hi Sargis,
In a test redocking a ligand in a protein-ligand system using Pyrx 0.9.2 on Fedora Linux 20 64bit, I realized there was a change in the results analysis tab (figure attached).
I have two questions:
1) How do I know which pose of the ligand is being presented, since there is no pose selected on the left tab?
2) How can I change the settings of the result analysis tab, to be as it was in the previous version?

I await your reply,

Regards,

Flavio
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Re: Doubt about results in Pyrx 0.9.2 version

Postby sargis » Mon May 26, 2014 6:18 pm

Hi Flavio,

Thank you for the message.
oivalf_nix wrote:1) How do I know which pose of the ligand is being presented, since there is no pose selected on the left tab?

Good question. The pose of the ligand shown is the last pose selected before switching to a different ligand. If you used down arrow key to scroll down this table, then the last pose of the ligand in the table will be shown on the screen. Please let me know if this makes sense.
oivalf_nix wrote:2) How can I change the settings of the result analysis tab, to be as it was in the previous version?

As far as I recall, the result analysis tab is the same as in the previous version. Could you please let me know which change you are refereeing compered to the previous version.

Thanks,
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Re: Doubt about results in Pyrx 0.9.2 version

Postby oivalf_nix » Mon May 26, 2014 8:25 pm

Hi Sargis,
Thank you for your answer.
Maybe I did not make myself clear. Sorry for that.

I select the first pose in the result table and then it appears on the screen. Ok, it is what I want.
However, I want now to unselect this pose to make it disapear off the display, in order to evaluate ONLY the second pose from the result table.
I want to investigate each pose at a time, as it was in Pyrx 0.9.

You will see in the picture attached, there are a lot of poses in the display although no one be selected in the Molecules tab. This fact makes the analysis of the individual pose very confused.

How can I erase all of then and put only the selected pose in the display?

Regards,

Flavio
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Re: Doubt about results in Pyrx 0.9.2 version

Postby sargis » Tue May 27, 2014 3:02 am

Hi Flavio,

Thank you for the info and sorry about that. I think I see what's going on now. It seems that the macromolecule had capital letters, which caused PyRx to create a new molecule and add _ to its name every time a new conformation is selected. I've prepared a new update to fix this. Please use PyRx > Help > Check for Updates... menu and let me know if that fixes this.

Thank you for using PyRx!
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Re: Doubt about results in Pyrx 0.9.2 version

Postby oivalf_nix » Tue May 27, 2014 4:26 pm

Hi Sargis,
Thank you for the update.
Pyrx is working very fine now.

Best regards,

Flavio
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