Phenix/pymol

[root@rockylinux9 ~]# mkdir -p /apps/src && cd /apps/src
[root@rockylinux9 src]# tar xf /Public/em/phenix-installer-1.21.2-5419-intel-linux-2.6-x86_64-centos6.tar.gz
[root@rockylinux9 src]# cd phenix-installer-1.21.2-5419-intel-linux-2.6-x86_64-centos6/
[root@rockylinux9 phenix-installer-1.21.2-5419-intel-linux-2.6-x86_64-centos6]# ./install --prefix=/apps
[root@rockylinux9 phenix-installer-1.21.2-5419-intel-linux-2.6-x86_64-centos6]# cd
[root@rockylinux9 ~]# rm -rf /apps/src/phenix-installer-1.21.2-5419-intel-linux-2.6-x86_64-centos6

[root@rockylinux9 ~]# dnf install epel-release
[root@rockylinux9 ~]# dnf install xcb-util-wm xcb-util-image xcb-util-keysyms xcb-util-renderutil
[root@rockylinux9 ~]# dnf --enablerepo=devel install cmake netcdf-devel glew-devel libpng-devel libxml2-devel freetype-devel catch2-devel msgpack-devel glm-devel
[root@rockylinux9 ~]# dnf install libXext-devel libXrender-devel libXrandr-devel libXcursor-devel libXi-devel fontconfig-devel  mesa-libGL-devel libX11-devel expat-devel libXcomposite-devel libXfixes-devel dbus-devel libXScrnSaver-devel
 
 
[root@rockylinux9 ~]# cd /apps/src/
 
[root@rockylinux9 src]# git clone --depth 1 https://github.com/rcsb/mmtf-cpp.git
[root@rockylinux9 src]# cp -R mmtf-cpp/include/mmtf* /usr/local/include
 
[root@rockylinux9 src]# git clone https://github.com/schrodinger/pymol-open-source
[root@rockylinux9 src]# cd pymol-open-source/
[root@rockylinux9 pymol-open-source]#
[root@rockylinux9 pymol-open-source]# git branch --all
* master
  remotes/origin/HEAD -> origin/master
  remotes/origin/cpp11
  remotes/origin/master
  remotes/origin/py2
  remotes/origin/ubuntu24
[root@rockylinux9 pymol-open-source]#
[root@rockylinux9 pymol-open-source]# git checkout remotes/origin/py2
 
[root@rockylinux9 pymol-open-source]# LDFLAGS="-L/apps/phenix-1.21.2-5419/conda_base/lib" /apps/phenix-1.21.2-5419/conda_base/bin/python setup.py install --prefix=/apps/phenix_pymol

[root@rockylinux9 ~]# cd /apps/src/
[root@rockylinux9 src]# wget https://www.riverbankcomputing.com/static/Downloads/sip/4.19.25/sip-4.19.25.tar.gz
[root@rockylinux9 src]# tar xf sip-4.19.25.tar.gz
[root@rockylinux9 src]# cd sip-4.19.25/
 
[root@rockylinux9 sip-4.19.25]# 
[root@rockylinux9 sip-4.19.25]# /apps/phenix-1.21.2-5419/conda_base/bin/python ./configure.py
[root@rockylinux9 sip-4.19.25]# make; make install

[root@rockylinux9 ~]# cd /apps/src/
[root@rockylinux9 src]# wget https://www.riverbankcomputing.com/static/Downloads/PyQt4/4.12.3/PyQt4_gpl_x11-4.12.3.tar.gz

[root@rockylinux9 ~]# cd /apps/src/
[root@rockylinux9 src]# wget https://download.qt.io/archive/qt/4.8/4.8.7/qt-everywhere-opensource-src-4.8.7.tar.gz
[root@rockylinux9 src]# tar xf qt-everywhere-opensource-src-4.8.7.tar.gz
[root@rockylinux9 src]# cd qt-everywhere-opensource-src-4.8.7/
[root@rockylinux9 qt-everywhere-opensource-src-4.8.7]#
[root@rockylinux9 qt-everywhere-opensource-src-4.8.7]# QMAKE_CFLAGS="QT_NO_CUPS" QMAKE_CXXFLAGS="QT_NO_CUPS" ./configure -prefix /opt/qt4 -opensource -confirm-license -nomake examples -nomake demos -no-openssl -no-cups
 :
Build .................. libs tools docs translations
Configuration ..........  release largefile stl precompile_header mmx 3dnow sse sse2 sse3 ssse3 sse4_1 sse4_2 avx  minimal-config small-config medium-config large-config full-config qt3support accessibility opengl shared reduce_exports ipv6 clock-gettime clock-monotonic mremap getaddrinfo ipv6ifname getifaddrs inotify system-png png system-freetype system-zlib iconv glib dbus xshape xsync xrender mitshm fontconfig xkb icu concurrent multimedia audio-backend svg script scripttools declarative release
Debug .................. no
Qt 3 compatibility ..... yes
QtDBus module .......... yes (run-time)
QtConcurrent code ...... yes
QtGui module ........... yes
QtScript module ........ yes
QtScriptTools module ... yes
QtXmlPatterns module ... no
Phonon module .......... no
Multimedia module ...... auto
SVG module ............. yes
WebKit module .......... no
JavaScriptCore JIT ..... To be decided by JavaScriptCore
Declarative module ..... yes
Declarative debugging ...yes
Support for S60 ........ no
Symbian DEF files ...... no
STL support ............ yes
PCH support ............ yes
MMX/3DNOW/SSE/SSE2/SSE3. yes/yes/yes/yes/yes
SSSE3/SSE4.1/SSE4.2..... yes/yes/yes
AVX..................... yes
Graphics System ........ default
IPv6 support ........... yes
IPv6 ifname support .... yes
getaddrinfo support .... yes
getifaddrs support ..... yes
Accessibility .......... yes
NIS support ............ no
CUPS support ........... no
Iconv support .......... yes
Glib support ........... yes
GStreamer support ...... no
PulseAudio support ..... no
Large File support ..... yes
GIF support ............ plugin
TIFF support ........... plugin (qt)
JPEG support ........... plugin (qt)
PNG support ............ yes (system)
MNG support ............ plugin (qt)
zlib support ........... system
Session management ..... no
OpenGL support ......... yes (Desktop OpenGL)
OpenVG support ......... no
NAS sound support ...... no
XShape support ......... yes
XVideo support ......... no
XSync support .......... yes
Xinerama support ....... no
Xcursor support ........ runtime
Xfixes support ......... runtime
Xrandr support ......... runtime
Xrender support ........ yes
Xi support ............. runtime
MIT-SHM support ........ yes
FontConfig support ..... yes
XKB Support ............ yes
immodule support ....... yes
GTK theme support ...... no
SQLite support ......... plugin (qt)
OpenSSL support ........ no
Alsa support ........... no
ICD support ............ no
libICU support ......... yes
Use system proxies ..... no
 :