CCTBX: Difference between revisions

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=== Incentive PyMOL ===
=== Incentive PyMOL ===


Using cctbx with Incentive PyMOL 2.x should become easier once the cctbx project provides conda packages.
Create a [https://repo.continuum.io/miniconda/ conda] environment with [https://anaconda.org/schrodinger/pymol schrodinger::pymol] and [https://anaconda.org/conda-forge/cctbx-base conda-forge::cctbx-base].
See https://github.com/cctbx/cctbx_project/issues/9


==== Linux ====
On Linux and Windows:


Confirmed procedure to get this working on Linux with CCTBX build '''dev-1723''', which is based on conda:
<syntaxhighlight lang="bash">conda create -n env1 schrodinger::pymol conda-forge::cctbx-base</syntaxhighlight>


# Download cctbx from http://cci.lbl.gov/cctbx_build/
On macOS, you also need [https://anaconda.org/schrodinger/pymol schrodinger::tk] and [https://www.xquartz.org/ XQuartz]:
# Install cctbx: <code>./install --prefix=$HOME/local</code>
# Install [https://repo.continuum.io/miniconda/ Miniconda]
# Install '''pymol''' with '''conda''' into the '''cctbx environment''':<syntaxhighlight lang="bash">$HOME/miniconda3/bin/conda install -p $HOME/local/cctbx-dev-1723/conda_base -c schrodinger -c conda-forge pymol</syntaxhighlight>
# Activate cctbx: <code>source $HOME/local/cctbx-dev-1723/cctbx_env.sh</code>
# Run PyMOL with: <code>cctbx.python -m pymol</code>


==== Windows ====
<syntaxhighlight lang="bash">conda create -n env1 schrodinger::pymol conda-forge::cctbx-base schrodinger::tk</syntaxhighlight>
 
Confirmed procedure to get this working on Windows with CCTBX build '''dev-1725''', which is based on conda:
 
# Download cctbx from http://cci.lbl.gov/cctbx_build/
# Extract ZIP file (e.g. to <code>F:\cctbx-installer-dev-1725-intel-windows-x86_64</code>)
# Install [https://repo.continuum.io/miniconda/ Miniconda]
# Install '''pymol''' with '''conda''' into the '''cctbx environment''': <code>conda install -p F:\cctbx-installer-dev-1725-intel-windows-x86_64\conda_base -c schrodinger -c conda-forge pymol</code>
# Activate cctbx: <code>call F:\cctbx-installer-dev-1725-intel-windows-x86_64\cctbx_env.bat</code>
# Run PyMOL with: <code>cctbx.python -m pymol</code>


=== Open-Source PyMOL ===
=== Open-Source PyMOL ===

Latest revision as of 04:22, 24 September 2020

This page describes how to use the Computational Crystallography Toolbox (cctbx) with PyMOL.

cctbx and PyMOL need to be compiled with the same Python distribution, otherwise they won't be compatible.

Incentive PyMOL

Create a conda environment with schrodinger::pymol and conda-forge::cctbx-base.

On Linux and Windows: 

conda create -n env1 schrodinger::pymol conda-forge::cctbx-base

On macOS, you also need schrodinger::tk and XQuartz: 

conda create -n env1 schrodinger::pymol conda-forge::cctbx-base schrodinger::tk

Open-Source PyMOL

See CCTBX-fedora32.

Retrieved from "https://pymolwiki.org/index.php?title=CCTBX&oldid=13326"