Unable to open pymol after successful installation

[dyodyo121]

I am currently running Ubuntu 22.04 and trying to install PyMol open source. I have successfully installed it but I cannot open the program. Can you help me with my problem?

[ye11owSub]

Hey @dyodyo121 could you please provide an error message? and how exactly did you install pymol?

[dyodyo121]

Hello,

There's no error message. I successfully installed pymol and check if it was placed in usr/bin which it was. It's just that the program is not opening at all.

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From: ye11owSub @.> Sent: Monday, 19 August 2024 11:35 pm To: schrodinger/pymol-open-source @.> Cc: dyodyo121 @.>; Mention @.> Subject: Re: [schrodinger/pymol-open-source] Unable to open pymol after successful installation (Issue #392)

Hey @dyodyo121https://github.com/dyodyo121 could you please provide an error message? and how exactly did you install pymol?

— Reply to this email directly, view it on GitHubhttps://github.com/schrodinger/pymol-open-source/issues/392#issuecomment-2296869316, or unsubscribehttps://github.com/notifications/unsubscribe-auth/APYLB5Q735MGHPVLZFG74DDZSIGFXAVCNFSM6AAAAABMX4VZNCVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMZDEOJWHA3DSMZRGY. You are receiving this because you were mentioned.Message ID: @.***>

[ye11owSub]

Hmm, that sounds strange. Could you please tell me more about how you installed and ran it?

[dyodyo121]

Here were the following approaches that I did:

1. followed the git clone instructions (https://wiki.pymol.org/index.php/Linux_Install) 2. installed via conda-forge (https://anaconda.org/conda-forge/pymol-open-source) --> I installed it through conda base 3. installed through pip (https://github.com/schrodinger/pymol-open-source/blob/master/INSTALL)

I used to successfully download pymol-open-source by using git clone when I was on Ubuntu 20.04 LTS so I also found it strange. When I installed Ubuntu 22.04 on a new system, all of my software essentially messed up big time due to backward compatibility issues. I assumed that pymol-open-source would not cause issues because the latest version is already written in python 3.

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From: ye11owSub @.> Sent: Monday, 19 August 2024 11:54 pm To: schrodinger/pymol-open-source @.> Cc: dyodyo121 @.>; Mention @.> Subject: Re: [schrodinger/pymol-open-source] Unable to open pymol after successful installation (Issue #392)

Hmm, that sounds strange. Could you please tell me more about how you installed and ran it?

— Reply to this email directly, view it on GitHubhttps://github.com/schrodinger/pymol-open-source/issues/392#issuecomment-2296907219, or unsubscribehttps://github.com/notifications/unsubscribe-auth/APYLB5R6XH3O3IBYQR5UED3ZSIIKTAVCNFSM6AAAAABMX4VZNCVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMZDEOJWHEYDOMRRHE. You are receiving this because you were mentioned.Message ID: @.***>

[ye11owSub]

installed through pip (https://github.com/schrodinger/pymol-open-source/blob/master/INSTALL)

Could you please provide me with the logs that were generated after you ran the pip install -v . command in the pymol directory?

[dyodyo121]

Hi,

I could not locate the folder which was the installation path for pip install. I tried installing it using Ubuntu software (pymol-oss) and it worked. I am not sure what is wrong with the pip install function.

Sent from Outlook for Androidhttps://aka.ms/AAb9ysg

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From: ye11owSub @.> Sent: Tuesday, August 20, 2024 12:51:19 AM To: schrodinger/pymol-open-source @.> Cc: dyodyo121 @.>; Mention @.> Subject: Re: [schrodinger/pymol-open-source] Unable to open pymol after successful installation (Issue #392)

installed through pip (https://github.com/schrodinger/pymol-open-source/blob/master/INSTALL)

Could you please provide me with the logs that were generated after you ran the pip install -v . command in the pymol directory?

— Reply to this email directly, view it on GitHubhttps://github.com/schrodinger/pymol-open-source/issues/392#issuecomment-2297010217, or unsubscribehttps://github.com/notifications/unsubscribe-auth/APYLB5XHKWEMW66D3SZT3Y3ZSIPAPAVCNFSM6AAAAABMX4VZNCVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMZDEOJXGAYTAMRRG4. You are receiving this because you were mentioned.Message ID: @.***>

[ye11owSub]

@dyodyo121

To install the pymol project to any path you choose, you will need to specify the path using the --prefix flag

Without the --prefix flag, pymol will be installed to your python site-packages directory (like any other python package installed using pip). You can verify this by running the pip list command.

[ye11owSub]

@dyodyo121 try simply running pymol command in your terminal

[ye11owSub]

@JarrettSJohnson I assume this ticket can be closed