Re: [PyMOL] PLEASE HELP

[Kyle M. <kmo...@fa...>]

Thank you SO MUCH. My computer is going into overdrive. I want to use another terminal, but I’ve spent all last night and all day today trying to figure it out.

My phone number is 562-360-7713.

I’m really doing whatever it takes to make this work. Thank you again.

Kyle

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________________________________
From: Jarrett Johnson <jar...@sc...>
Sent: Monday, March 27, 2023 4:23:30 PM
To: Kyle Moorman <kmo...@fa...>
Cc: pym...@li... <pym...@li...>
Subject: Re: [PyMOL] PLEASE HELP

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Hi Kyle,

The approach you listed looks about right to me. Using conda commands from the PyMOL commandline in the bundles don't seem to be working in those builds, but should be fine if you use another terminal. Either way, I will reach out to you directly.

Best,
Jarrett J.

On Mon, Mar 27, 2023 at 3:46 PM Kyle Moorman via PyMOL-users <pym...@li...<mailto:pym...@li...>> wrote:

To whom it may concern,



While I am a licensed user of PyMol, he...@sc...<mailto:he...@sc...> has still not responded to me. I have some very technical installation questions which upon trying to solve on my own is only making the problem worse.



Below is all the information I have and what I’ve sent to he...@sc...<mailto:he...@sc...> This has truly been a huge impediment to my work and your help in this matter would be greatly appreciated. Currently conda is crashing every time I try to open it and the instructions I’ve found on pymolwiki as well as various other sites I’ve come across are not very clear at all. Below is the message I sent to he...@sc...<mailto:he...@sc...>  Could you help please? Thanks in advance:



PyMOL 2.5.4
Windows-10-10.0.19041-SP0
ATI Technologies Inc.
AMD Radeon(TM) HD8490
4.5.13399 Compatibility Profile Context 15.201.1151.1008
PyMOL Invoice #49406
01-mar-2024

Filename of downloaded installer: PyMOL-2.5.4_404-Win64-portable-py37







I’m requesting help once more. An extension is not downloading for me. Please let me know if there is any other information I need to provide in order to receive installation help. This has thus far been a very unsatisfactory experience. Below is the email I sent before:



To whom it may concern,

I have used the following commands in attempt to download psico:

I used this file path:
"C:\Users\admin\PyMOL\condabin\conda.bat"

In order to install this code:

conda install -c schrodinger pymol
conda install -c schrodinger pymol-psico
conda install -c rdkit rdkit
conda install -c speleo3 csb

I am now having trouble using the commands in this code within the command line in PyMol. I believe that I need to use some sort of API in order to use the commands from psico. I am installing these packages specifically to use the 'mcsalign' function to calculate better rmsd's based off structural overlap of molecules I'm studying in school right now.


I have version of 2.5.4 of PyMol and 2.7 version of Python. Could you please provide help as to how specifically download an API so I may employ the commands from psico? This function would be incredibly useful but I'm getting very caught up with the installation. If there is someone I can share my screen with so I can get this going, I'd really appreciate it. I'm really stuck and in need of help.

Thanks so much in advance,

Kyle



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--

Jarrett Johnson | Senior Developer, PyMOL

[https://drive.google.com/uc?id=1zOlB9fluGZyuInRUQgKsdjtjpR5L9z6R&export=download]