Decomposition analysis pymol visualization.

[Raj Choudhary]

Hello

I am getting this error message while trying to visualize the results of decomposition analysis (protein-ligand complex per-residue energy representation) on pymol. I have pymol installed in my system as wel.Please find attached the error message. 

How to solve this problem?

Thank you

Best regards

[Mario Sergio Valdes]

As the error says, you haven't any PyMOL executable in the PATH. You can install a PyMOL version in three ways:

- Installing it from the Linux repository (make sure that the version is 2.x) -> sudo apt install pymol

- Installing it from conda (sometimes it is not functional) -> conda install -c conda-forge pymol-open-source

- Compiling it yourself from the GitHub repository (it is a little complicated) -> https://github.com/schrodinger/pymol-open-source

Let me know any doubt

[Raj Choudhary]

Sir I have PyMOL already installed in my Linux system. However, it is still showing that error. Do I need to any how link pymol with gmx_MMPBSA?

Best regards

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[Mario Sergio Valdes]

gmx_MMPBSA searches all PyMOL executables in the PATH. For some reason, it does not find it. It could be that it is not directly in the PATH or that it is conditional.

Could you show me the output of this command line, please?

which pymol

[Raj Choudhary]

Sir, the output obtained on command line is as follows:

Warning: Ignoring XDG_SESSION_TYPE=wayland on Gnome. Use QT_QPA_PLATFORM=wayland to run on Wayland anyway.
libGL error: MESA-LOADER: failed to open iris: /usr/lib/dri/iris_dri.so: cannot open shared object file: No such file or directory (search paths /usr/lib/x86_64-linux-gnu/dri:\$${ORIGIN}/dri:/usr/lib/dri, suffix _dri)
libGL error: failed to load driver: iris
libGL error: MESA-LOADER: failed to open swrast: /usr/lib/dri/swrast_dri.so: cannot open shared object file: No such file or directory (search paths /usr/lib/x86_64-linux-gnu/dri:\$${ORIGIN}/dri:/usr/lib/dri, suffix _dri)
libGL error: failed to load driver: swrast

However, this output is persisting on the terminal right from the opening of gmx_MMPBS_ana and no new output is further obtained upon trying to open the PyMOL visualization. While other features of gmx_MMPBSA_ana seem to be working fine, it's only the PyMOL visualization part that I am unable to access.

My version of PyMOL is 2.5.0 Open-Source.

Best regards

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[Mario Sergio Valdes]

The previous command (which pymol) shows the path of the preferred pymol in the PATH. I don't see how this command shows all this information.
Please show me the output of the command (which pymol)
To solve these warnings check this section (https://valdes-tresanco-ms.github.io/gmx_MMPBSA/dev/Q%26A/OS_issues/#solution_2) and this (https://github.com/Valdes-Tresanco-MS/gmx_MMPBSA/issues/208#issuecomment-1082037051)

[Raj Choudhary]

Dear Sir

Pardon me as I am not quite able to understand what exactly you are referring to.

I am trying to access the PyMOL visualizer feature from the gmx_MMPBSA_ana GUI by clicking on the PyMOL icon shown alongside TDC or SDC (as shown in the attached image 1). However, immediately upon clicking this PyMOL icon on the GUI, I am getting this message (image 2) that says - PyMOL not found! Make sure PyMOL is in the path!

Please let me know if you need any other information. I have PyMOL version 2.5 already installed in my system.

Best regards

Raj

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[Mario Sergio Valdes]

gmx_MMPBSA uses an external PyMOL for this visualization. It means that there must be a PyMOL executable accessible in the PATH (environment variable that defines the accessible paths of executables in Linux). It is possible to have multiple versions or installations of a program in Linux, without any of them being accessible in the PATH. In your case, gmx_MMPBSA does not find any PyMOL executable in the PATH. which pymol command will show you whether or not any PyMOL exists in the PATH. If the output is empty, then you must make PyMOL available in the PATH, either by creating a symbolic link or by adding the bin folder containing the PyMOL executable.
Also, you can install PyMOL in the conda environment of gmx_MMPBSA to not worry about PyMOL on the system.
Please, show me the output of:

which pymol

[Raj Choudhary]

Dear Sir

Thank you so much for your detailed explanation. I could resolve the issue as per your guidance.

Best regards

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[Isaac Silverman]

Hi,

I am experiencing a similar issue. I input which pymol and received the following: /usr/bin/pymol

When I press on the pymol icon in the gmx_MMPBSA_ana options, I receive a little spinning loading wheel which never opens anything. How would I fix this to be able to access pymol through gmx_MMPBSA_ana?

Thank you in advance

[Mario Sergio Valdes]

Please, check this issue https://github.com/Valdes-Tresanco-MS/gmx_MMPBSA/issues/331

Let me know if works four you

[Isaac Silverman]

Thanks! I found the pymol file to edit, however, when I try to save the change the file won't let me save it because it says it is a read only file. I tried to change the properties to make it editable, but there is a permission lock on it saying I cannot make it editable because I am not the owner. It says someone named root is the owner. Do you know what I could do to be able to make the edit?

[Mario Sergio Valdes]

You must use the sudo or root permission to edit it. 

[Isaac Silverman]

Thank you, I was able to get it working by doing that.