本家様 http://pymol.org/
open sourceでソースコードが提供されてます https://github.com/schrodinger/pymol-open-source
コンパイルせずに使えるバージョンは、本家様から入手可能で、open source版よりも機能が強化されてますが、有償です。
下準備 †
[root@rockylinux9 ~]# dnf install epel-release
[root@rockylinux9 ~]# dnf install --enablerepo=devel python3-devel platform-python-devel glew-devel glm-devel netcdf-devel libpng-devel libxml2-devel freetype-devel python3-qt5
(rockylinux8なら)
dnf install --enablerepo=powertools,epel python3-devel platform-python-devel glew-devel glm-devel netcdf-devel python3-qt5 libpng-devel libxml2-devel freetype-devel
(centos7なら)
yum install --enablerepo=epel python3-devel glew-devel glm-devel netcdf-devel libpng-devel libxml2-devel freetype-devel python36-qt5
コンパイル †
PyMOLのソースコードをgithubから取得します.
[root@rockylinux9 ~]# mkdir -p /apps/src && cd /apps/src
[root@rockylinux9 src]# git clone https://github.com/schrodinger/pymol-open-source
[root@rockylinux9 src]# cd pymol-open-source/
[root@rockylinux9 pymol-open-source]# python3 setup.py build
[root@rockylinux9 pymol-open-source]# python3 setup.py install --prefix=/apps/PyMOL
これで完了.
呼び出すpymolファイルの中身はこんな感じ
[root@rockylinux9 ~]# cat /apps/PyMOL/bin/pymol
#!/bin/sh
exec "/usr/bin/python3" "/apps/PyMOL/lib64/python3.9/site-packages/pymol/__init__.py" "$@"
[root@rockylinux9 ~]#
python3で実行される
*稀に「/usr/bin/python3」が「/usr/local/bin/python3」とかになる場合があるようで要注意
[saber@rockylinux9 ~]$ /apps/PyMOL/bin/pymol
めも †
windowsPCにXサーバを入れて画面表示する際はMobaXterm経由なら大丈夫。Xming経由では起動しない(200715現在)
Xming経由でのエラー内容
[illya@centos8 ~]$ /apps/pymol/bin/pymol
qt.qpa.xcb: could not connect to display
qt.qpa.plugin: Could not load the Qt platform plugin "xcb" in "" even though it was found.
This application failed to start because no Qt platform plugin could be initialized. Reinstalling the application may fix this problem.
Available platform plugins are: eglfs, linuxfb, minimal, minimalegl, offscreen, vnc, xcb.
Aborted (core dumped)
[illya@centos8 ~]$
MobaXterm経由なら表示はできているが、下記エラーが表示される。
[illya@centos8 ~]$ /apps/pymol/bin/pymol
PyMOL(TM) Molecular Graphics System, Version 2.5.0a0.
Copyright (c) Schrodinger, LLC.
All Rights Reserved.
Created by Warren L. DeLano, Ph.D.
PyMOL is user-supported open-source software. Although some versions
are freely available, PyMOL is not in the public domain.
If PyMOL is helpful in your work or study, then please volunteer
support for our ongoing efforts to create open and affordable scientific
software by purchasing a PyMOL Maintenance and/or Support subscription.
More information can be found at "http://www.pymol.org".
Enter "help" for a list of commands.
Enter "help <command-name>" for information on a specific command.
Hit ESC anytime to toggle between text and graphics.
qt.qpa.xcb: QXcbConnection: XCB error: 145 (Unknown), sequence: 175, resource id: 0, major code: 139 (Unknown), minor code: 20
Detected OpenGL version 3.1. Shaders available.
Geometry shaders not available
Detected GLSL version 1.40.
OpenGL graphics engine:
GL_VENDOR: VMware, Inc.
GL_RENDERER: llvmpipe (LLVM 9.0.0, 256 bits)
GL_VERSION: 3.1 Mesa 19.3.4
Detected 4 CPU cores. Enabled multithreaded rendering.
[illya@centos8 ~]$
これはここを参照して回避できた
https://stackoverflow.com/questions/51218417/qxcbconnection-xcb-error-145-unknown-error-message-starting-spyder-with-moba
EnvironmentModules †
「/apps/modulefiles/PyMOL」として
#%Module1.0
set pymol /apps/PyMOL
set-alias pymol $pymol/bin/pymol
プラグイン(APBS GUI) †
(入れる場所の確認)
[root@rockylinux9 ~]# ls /apps/PyMOL/lib64/python3.9/site-packages/pmg_tk/startup/
__init__.py __pycache__
[root@rockylinux9 ~]#
[root@rockylinux9 ~]# git clone https://github.com/YoshitakaMo/pymolplugin.git
[root@rockylinux9 ~]# cp -arp ~/pymolplugin/* /apps/PyMOL/lib64/python3.9/site-packages/pmg_tk/startup/
[root@rockylinux9 ~]# ls -l /apps/PyMOL/lib64/python3.9/site-packages/pmg_tk/startup/
total 8
drwxr-xr-x. 2 root root 41 Apr 13 19:33 align_gui
drwxr-xr-x. 2 root root 104 Apr 13 19:33 apbs_gui
drwxr-xr-x. 2 root root 49 Apr 13 19:33 excelexporter
-rw-r--r--. 1 root root 1454 Apr 13 19:28 __init__.py
drwxr-xr-x. 2 root root 40 Apr 13 19:33 lightingsettings_gui
drwxr-xr-x. 2 root root 41 Apr 13 19:33 morph_gui
drwxr-xr-x. 2 root root 37 Apr 13 19:34 __pycache__
-rw-r--r--. 1 root root 1082 Apr 13 19:33 README.md
[root@rockylinux9 ~]#
PyMOLを立ち上げて、メニューバーを確認してみる
次に表面電荷を計算するプログラムを導入します. pdb2pqr と APBS が必要で pdb2pqr はpipで入るそうな. もう片方(APBS)はmake testに python 3.6 が必要らしい.
なのでpyenv/anaconda環境でconda実行環境を１つ作って構築してみた
git clone https://github.com/yyuu/pyenv.git /apps/pyenv
export PYENV_ROOT=/apps/pyenv
export PATH=$PYENV_ROOT/bin:$PATH
pyenv install anaconda3-2023.03
pyenv global anaconda3-2023.03
export PATH=$PYENV_ROOT/versions/anaconda3-2023.03/bin/:$PATH
conda update conda
(既にpyenv/anaconda環境があるなら)
export PYENV_ROOT=/apps/pyenv
export PATH=$PYENV_ROOT/bin:$PATH
export PATH=$PYENV_ROOT/versions/anaconda3-2023.03/bin/:$PATH
としたうえで、
[root@rockylinux9 ~]# conda create -n pdb2pqr pip python=3.6
[root@rockylinux9 ~]# source activate pdb2pqr
(pdb2pqr) [root@rockylinux9 ~]# pip install pdb2pqr
(pdb2pqr) [root@rockylinux9 ~]# dnf --enablerepo=devel install suitesparse-devel libtirpc-devel
(pdb2pqr) [root@rockylinux9 ~]# cd /apps/src/
(pdb2pqr) [root@rockylinux9 src]# git clone https://github.com/Electrostatics/apbs
(pdb2pqr) [root@rockylinux9 src]# cd apbs/
(pdb2pqr) [root@rockylinux9 apbs]# mkdir build ; cd build
(pdb2pqr) [root@rockylinux9 build]# cmake .. -DCMAKE_INSTALL_PREFIX=/apps/apbs -DAPBS_STATIC_BUILD=OFF
(pdb2pqr) [root@rockylinux9 build]# make; make install
これで
pdb2pqr は「/apps/pyenv/versions/anaconda3-2023.03/envs/pdb2pqr/bin/pdb2pqr30」
APBS は「/apps/apbs/bin/apbs」
と指定して実行できます. 事前にLD_LIBRARY_PATHに「/apps/apbs/lib64」を入れる必要あり
プラグイン(APBS GUI) on rockylinux8 †
プラグインメニューのところまでは同じで、それ以降
その前に追加パッケージを入れます
dnf --enablerepo=powertools install suitesparse-devel libtirpc-devel cmake openblas-threads openblas-devel
dnf --enablerepo=powertools install metis-devel
dnf --enablerepo=powertools install boost-devel eigen3-devel (-DENABLE_GEOFLOW=ONなら)
dnf --enablerepo=powertools install swig (-DENABLE_PYTHON=ONなら + conda install pybind11)
その後で
[root@rockylinux ~]# conda create -n pdb2pqr pip python=3.6
[root@rockylinux ~]# source activate pdb2pqr
(pdb2pqr) [root@rockylinux ~]# pip install pdb2pqr
[引き続き APBS のインストール]
(pdb2pqr) [root@rockylinux ~]# cd /apps/src
(pdb2pqr) [root@rockylinux src]# git clone https://github.com/Electrostatics/apbs
(pdb2pqr) [root@rockylinux src]# cd apbs/
(pdb2pqr) [root@rockylinux apbs]# mkdir build ; cd build
(pdb2pqr) [root@rockylinux build]# cmake .. -DCMAKE_INSTALL_PREFIX=/apps/apbs -DAPBS_STATIC_BUILD=OFF \
-DENABLE_GEOFLOW=ON \
-DENABLE_BEM=ON \
-DENABLE_OPENMP=ON \
-DENABLE_PBAM=OFF \
-DENABLE_PBSAM=OFF \
-DENABLE_PYTHON=OFF \
-DENABLE_TESTS=ON
(pdb2pqr) [root@rockylinux build]# make -j 20 ; make install ; PATH=/apps/apbs/bin:$PATH make test
プラグイン(APBS GUI) on centos7 †
プラグインメニューのところまでは同じで、それ以降
その前に追加パッケージを入れます
yum install centos-release-scl-rh
yum install devtoolset-11
yum install --enablerepo=epel cmake3
yum install suitesparse-devel libtirpc-devel openblas-threads openblas-devel boost-devel eigen3-devel python3-devel
source scl_source enable devtoolset-11
その後で
[root@centos7 ~]# conda create -n pdb2pqr pip python=3.6
[root@centos7 ~]# source activate pdb2pqr
(pdb2pqr) [root@centos7 ~]# pip install pdb2pqr
[引き続き APBS のインストール]
(pdb2pqr) [root@centos7 ~]# cd /apps/src/
(pdb2pqr) [root@centos7 src]# git clone https://github.com/Electrostatics/apbs
(pdb2pqr) [root@centos7 src]# cd apbs/
(pdb2pqr) [root@centos7 apbs]# mkdir build ; cd build
(pdb2pqr) [root@centos7 build]# which gcc
/opt/rh/devtoolset-11/root/usr/bin/gcc
(pdb2pqr) [root@centos7 build]# cmake3 .. -DCMAKE_INSTALL_PREFIX=/apps/apbs -DAPBS_STATIC_BUILD=OFF \
-DENABLE_GEOFLOW=ON \
-DENABLE_BEM=ON \
-DENABLE_OPENMP=ON \
-DENABLE_PBAM=OFF \
-DENABLE_PBSAM=OFF \
-DENABLE_PYTHON=OFF\
-DENABLE_TESTS=ON
(pdb2pqr) [root@centos7 build]# make VERBOSE=1 ; make install ; PATH=/apps/apbs/bin:$PATH make test
テスト †
![[PukiWiki]](image/picc.png "[PukiWiki]")
