pymol-open-source

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Event listening

4

I found no way to listen for session loading, reinitialization, It would be useful for plugins like [Views](https://pymolwiki.org/index.php/Views). Something like Python's [`atexit`](https://docs.python.org/3/library/atexit.html) module: ```python from pymol import at_loading, at_reinit @at_loading...

pslacerda

How do you change the position of the color ramp?

8

When using cmd.ramp_new(), an object (a color bar) is generated that is located at the bottom center of the screen. How is this moved however? E.G. Have the color bar...

sam-mahdi

Why I can not convert amino acid using pymol?

6

Dear developer, I want to mutate all GLN&ASN to LEU of protein files to do some further research, but EVEN THOUGH the python scripts runs well without error, the output...

JonasLi-19

Bad Surface

6

Hi, Near Residue R181 (colored in orange) https://github.com/schrodinger/pymol-open-source/assets/8821384/286574d7-92f6-40c3-8efd-59ced6470542 the SES surface for protein 7BK1 (pdbid) computed by Pymol has defects. Please see the attached video. Is it a bug in...

wlincong

Pymol2 python package and PyMOL GUI contain different rotamer libraries

2

When loading the PDB 5D38 into the PyMOL GUI and using the mutagenesis wizard to mutate ARG 154 to TRP, the GUI displays 8 possible rotamers:  However, when I...

seb124

vtk-m: support latest release

2

can support be added for latest `VTK-m` release (currently v2.0.0)?

reneeotten

setup.py ignoring library search environment variables.

2

In the installation instructions it says: > Environment variables: > PREFIX_PATH Colon-delimited list of paths to search for headers and > libraries, e.g. $HOME/mmtf-cpp:$HOME/msgpack-c:/opt/local > CXX C++ compiler command >...

ErikPoppleton

ImportError: symbol not found in flat namespace '_PlugIOManagerFreeAll'

1

Hello I installed the latest version of pymol-open-source on my Macbook running Monterey 12.3.1 and Python 3.9 However, I run into an error while attempting to launch Pymol as follows...

gauravdiwan89

PyMOL-Error: can't find 'pymol.povray'

1

I am trying remove the dependency on Python from the generated PyMOL after setup install using pyinstaller. ```C:\PyMol\Lib\site-packages\pymol> pyinstaller .\__init__.py -n PyMol --clean --noconfirm``` After the dist folder is generated,...

eusebiu

Hi, I am using pymol to generate surface meshes from pdb source files. I would like to have the vertices in the same reference frame as the original pdb coordinates....

OliviaViessmann