Changing Output File Location?

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Changing Output File Location?

Postby kchemistry » Mon Nov 26, 2012 8:23 pm

Hello,

I am using PyRx to operate autodock vina and I'm wondering if it is possible to change the location of the output pdbqt files. Right now vina is putting them inside a 'macromolecules' folder that is inside of an invisible .mglTools folder that is in my username folder. I would like for the output files to go into a folder I created on my desktop. I am a student writing a protocol so other students can learn how to use vina to dock ligands and view them in pymol, so I must have a simple way of finding and opening the output pdbqt files.

Thanks for your time. Any help would be greatly appreciated.
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Re: Changing Output File Location?

Postby sargis » Tue Nov 27, 2012 12:51 am

kchemistry wrote:Hello,

I am using PyRx to operate autodock vina and I'm wondering if it is possible to change the location of the output pdbqt files. Right now vina is putting them inside a 'macromolecules' folder that is inside of an invisible .mglTools folder that is in my username folder. I would like for the output files to go into a folder I created on my desktop. I am a student writing a protocol so other students can learn how to use vina to dock ligands and view them in pymol, so I must have a simple way of finding and opening the output pdbqt files.

Thanks for your time. Any help would be greatly appreciated.


Thanks for the message. Please use PyRx -> Edit -> Preferences and change Workspace to your Desktop. I got this idea for workspace from Eclipse Open Source IDE. I haven't tested this feature (i.e. changing workspace) extensively, but it should work nonetheless.

Thank you for using PyRx!
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Re: Changing Output File Location?

Postby kchemistry » Wed Nov 28, 2012 4:53 pm

Hi,

Thank you for your fast response. I forgot to mention in my original post that I already did change my workspace under "preferences", but vina is still not sending my output files to the desktop.
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Re: Changing Output File Location?

Postby sargis » Thu Nov 29, 2012 9:16 pm

kchemistry wrote:Hi,

Thank you for your fast response. I forgot to mention in my original post that I already did change my workspace under "preferences", but vina is still not sending my output files to the desktop.

Thank you for the update. I just tested this with PyRx 0.9. on Linux and it works for me. What version of PyRx are you running and on which OS? Do you see Ligand and Macromolecules folder create on your Desktop after you change your workspace under "preferences" to Desktop?

Also, as a workaround, you can create a desktop shortcut or a link to point to any folder under ~/.mgltools/PyRx. If it turns out that this workspace is confusing feature to use or maintain, we can drop it from the future releases since it's one of the non-essential features of PyRx.
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Re: Changing Output File Location?

Postby kchemistry » Wed Dec 05, 2012 7:18 pm

Hey,

Ok, so I figured out my problem. I misunderstood what the pyrx output folder was all about. Apparently, it's just the pre-dock converted pdbqt files. So the reason I couldn't find the files in that folder was because I was clearing my pyrx scene, deleting ligands etc. in order to run the next thing before I checked the output folder, and apparently the files only exist in the folder for as long as they exist in pyrx.

The reason I was trying to locate these folders in the first place is because I was having a problem viewing docked ligand sdf files. Maybe I should start a new thread for this but I'll explain it here for now.

So I'm running a library (~1,500 compounds) against a search space on a single protein. When Vina is done docking, it allows me to download csv and sdf files. The csv files contain info for all of the ligands, but the sdf files only have docked images of the number 1 binding mode ligand, and none of the others. What I would like to do is be able to use Pymol to scan through all of the ligands (post-dock) in the library while my protein is open in the same session so I can see where the ligands are docking in the search space.

Any suggestions would be greatly appreciated.
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Re: Changing Output File Location?

Postby sargis » Thu Dec 06, 2012 3:17 am

kchemistry wrote:Ok, so I figured out my problem. I misunderstood what the pyrx output folder was all about. Apparently, it's just the pre-dock converted pdbqt files. So the reason I couldn't find the files in that folder was because I was clearing my pyrx scene, deleting ligands etc. in order to run the next thing before I checked the output folder, and apparently the files only exist in the folder for as long as they exist in pyrx.

The reason I was trying to locate these folders in the first place is because I was having a problem viewing docked ligand sdf files. Maybe I should start a new thread for this but I'll explain it here for now.

So I'm running a library (~1,500 compounds) against a search space on a single protein. When Vina is done docking, it allows me to download csv and sdf files. The csv files contain info for all of the ligands, but the sdf files only have docked images of the number 1 binding mode ligand, and none of the others. What I would like to do is be able to use Pymol to scan through all of the ligands (post-dock) in the library while my protein is open in the same session so I can see where the ligands are docking in the search space.

Any suggestions would be greatly appreciated.

Thanks for the update. Please use PyRx -> Edit -> Preferences -> Open Babel and set Number of Poses to Retain to 0 to save all the binding mode in the sdf.
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Re: Changing Output File Location?

Postby kchemistry » Tue Dec 11, 2012 6:51 pm

Hi there,

So, I followed your instructions exactly, and I'm still running into the same problem. In this case, I'm trying to obtain (post-dock) sdf files for 5 ligands. Whichever ligand I save as an sdf file first, it saves all of the other ligands as that structure as well. So I wind up with 5 sdf files of the exact same structure docked to my protein.

poses to retain.png
screen shot of me changing the poses to retain
poses to retain.png (46.33 KiB) Viewed 6525 times


Just to be clear, what I'm doing in order to save the sdf files is clicking on the desired binding mode in the vina wizard "analyze results" window, unclicking all other structures besides the desired ligand in the "molecules" tab, and clicking on the "save to sdf" icon in the upper right corner of the "analyze results" window.

Thanks
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Re: Changing Output File Location?

Postby sargis » Tue Dec 11, 2012 10:05 pm

kchemistry wrote:Hi there,

So, I followed your instructions exactly, and I'm still running into the same problem. In this case, I'm trying to obtain (post-dock) sdf files for 5 ligands. Whichever ligand I save as an sdf file first, it saves all of the other ligands as that structure as well. So I wind up with 5 sdf files of the exact same structure docked to my protein.

Just to be clear, what I'm doing in order to save the sdf files is clicking on the desired binding mode in the vina wizard "analyze results" window, unclicking all other structures besides the desired ligand in the "molecules" tab, and clicking on the "save to sdf" icon in the upper right corner of the "analyze results" window.

Thanks

"Save as SDF" saves docked poses from the Results tab; what you see in the Molecules tab has no effect on Save as SDF. Also, what you select in that table and elsewhere has no effect on "Save as SDF" as well. You can't selectively pick which modes you want to save in the sdf. It's either all the modes or a specific number of modes from each docking runs. You can, however, select specific poses and save them as PDB, one by one, through the Molecules tab.

Hope this clears up things a bit.
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Re: Changing Output File Location?

Postby kchemistry » Wed Dec 12, 2012 5:16 pm

Thank you, I was able to view the files in pymol by saving them as PDB using the macromolecules tab. I also now understand how "saving as sdf" works.
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