How to install PyMOL, Chimera and VMD in Fedora?
PyMOL
We have three ways to install PyMOL.
- Install from the source code, follow the wiki. This is sometimes a pita, sometimes it just works.
- Install it with the package manager of your Linux distribution
sudo dnf -y install pymol. The problem with this approach is that the version installed is not the latest and is the ‘educational version’. Debian-based distros, like Ubuntu, will have an older version than Fedora. The good thing is that it just works. - Get a license here and download
pymolfrom here. After that do:
cd ~/Downloads
tar xvf PyMOL*bz2
cd pymol
cd bin
./pymol
# If you want to run PyMOL from anywhere you have to make an alias
cd
echo "# PyMOL alias" >> .bashrc
echo "alias pymol='/home/`whoami`/Downloads/pymol/bin/pymol'" >> .bashrc
Warning: This
pymoldoes not work in Fedora 34. You only get a black screen. The error is the following:
libGL error: MESA-LOADER: failed to open iris: /home/murphy/Downloads/pymol/lib/python3.7/site-packages/pymol/../../../libstdc++.so.6: version `GLIBCXX_3.4.29' not found (required by /usr/lib64/dri/iris_dri.so) (search paths /usr/lib64/dri)
libGL error: failed to load driver: iris
libGL error: MESA-LOADER: failed to open iris: /home/murphy/Downloads/pymol/lib/python3.7/site-packages/pymol/../../../libstdc++.so.6: version `GLIBCXX_3.4.29' not found (required by /usr/lib64/dri/iris_dri.so) (search paths /usr/lib64/dri)
libGL error: failed to load driver: iris
libGL error: MESA-LOADER: failed to open swrast: /home/murphy/Downloads/pymol/lib/python3.7/site-packages/pymol/../../../libstdc++.so.6: version `GLIBCXX_3.4.29' not found (required by /usr/lib64/dri/swrast_dri.so) (search paths /usr/lib64/dri)
libGL error: failed to load driver: swrast
Update: I gotta say I bought an academic license for a year and supposedly you get documentation and support but the latter is really unnecessary and the documentation was way too old.
Chimera
Go here and download the appropriate installer for your machine. Then do…
cd ~/Downloads
chmod +x chimera*.bin
# run it
./chimera-1.15-linux_x86_64.bin
# Press enter three times and you are done
# Do an alias
cd
echo "#Chimera alias" >> .bashrc
echo "alias chimera='/home/murphy/.local/UCSF-Chimera64-1.15rc/bin/chimera'" >> .bashrc
chimerais a good alternative topymoland is free of charge for noncommercial use. The main disadvantage is that Chimera is no longer under active development, and is only updated for critical maintenance.
ChimeraX
chimeraX is going to substitute chimera. So far I am unable to install it.
[murphy@eva02 Downloads]$ sudo rpm -i ./ucsf-chimerax-1.2.5-1.el8.x86_64.rpm
[sudo] password for murphy:
error: Failed dependencies:
fftw-libs-single is needed by ucsf-chimerax-1.2.5-1.el8.x86_64
mesa-libOSMesa is needed by ucsf-chimerax-1.2.5-1.el8.x86_64
[murphy@eva02 Downloads]$ sudo dnf install ./ucsf-chimerax-1.2.5-1.el8.x86_64.rpm
Last metadata expiration check: 2:29:59 ago on Mon 31 May 2021 07:01:27 PM CDT.
Dependencies resolved.
================================================================================
Package Arch Version Repository Size
================================================================================
Installing:
ucsf-chimerax x86_64 1.2.5-1.el8 @commandline 307 M
Upgrading:
mesa-libGL x86_64 21.1.1-1.fc34 updates 171 k
mesa-libglapi x86_64 21.1.1-1.fc34 updates 55 k
Installing dependencies:
fftw-libs-single x86_64 3.3.8-10.fc34 fedora 953 k
mesa-libOSMesa x86_64 21.1.1-1.fc34 updates 3.1 M
Transaction Summary
================================================================================
Install 3 Packages
Upgrade 2 Packages
Total size: 311 M
Total download size: 4.3 M
Is this ok [y/N]: y
Downloading Packages:
(1/4): fftw-libs-single-3.3.8-10.fc34.x86_64.rp 588 kB/s | 953 kB 00:01
(2/4): mesa-libGL-21.1.1-1.fc34.x86_64.rpm 83 kB/s | 171 kB 00:02
(3/4): mesa-libglapi-21.1.1-1.fc34.x86_64.rpm 112 kB/s | 55 kB 00:00
(4/4): mesa-libOSMesa-21.1.1-1.fc34.x86_64.rpm 1.1 MB/s | 3.1 MB 00:02
--------------------------------------------------------------------------------
Total 1.1 MB/s | 4.3 MB 00:03
Running transaction check
Transaction check succeeded.
Running transaction test
The downloaded packages were saved in cache until the next successful transaction.
You can remove cached packages by executing 'dnf clean packages'.
Error: Transaction test error:
file /usr/lib/.build-id/34/aac32bb4d3c0f44e72e57cf253a871240a1154 from install of ucsf-chimerax-1.2.5-1.el8.x86_64 conflicts with file from package rstudio-1.4.1106-1.x86_64
file /usr/lib/.build-id/80/916a3578c4abf8d9433986b7ca87ee58797eb5 from install of ucsf-chimerax-1.2.5-1.el8.x86_64 conflicts with file from package rstudio-1.4.1106-1.x86_64
file /usr/lib/.build-id/ea/6a2369dae8e186543b5e0fa413cb7ee7058c84 from install of ucsf-chimerax-1.2.5-1.el8.x86_64 conflicts with file from package rstudio-1.4.1106-1.x86_64
[murphy@eva02 Downloads]$ dnf clean packages
0 files removed
[murphy@eva02 Downloads]$ sudo dnf install ./ucsf-chimerax-1.2.5-1.el8.x86_64.rpm
Last metadata expiration check: 2:30:45 ago on Mon 31 May 2021 07:01:27 PM CDT.
Dependencies resolved.
================================================================================
Package Arch Version Repository Size
================================================================================
Installing:
ucsf-chimerax x86_64 1.2.5-1.el8 @commandline 307 M
Upgrading:
mesa-libGL x86_64 21.1.1-1.fc34 updates 171 k
mesa-libglapi x86_64 21.1.1-1.fc34 updates 55 k
Installing dependencies:
fftw-libs-single x86_64 3.3.8-10.fc34 fedora 953 k
mesa-libOSMesa x86_64 21.1.1-1.fc34 updates 3.1 M
Transaction Summary
================================================================================
Install 3 Packages
Upgrade 2 Packages
Total size: 311 M
Is this ok [y/N]: y
Downloading Packages:
[SKIPPED] fftw-libs-single-3.3.8-10.fc34.x86_64.rpm: Already downloaded
[SKIPPED] mesa-libOSMesa-21.1.1-1.fc34.x86_64.rpm: Already downloaded
[SKIPPED] mesa-libGL-21.1.1-1.fc34.x86_64.rpm: Already downloaded
[SKIPPED] mesa-libglapi-21.1.1-1.fc34.x86_64.rpm: Already downloaded
Running transaction check
Transaction check succeeded.
Running transaction test
The downloaded packages were saved in cache until the next successful transaction.
You can remove cached packages by executing 'dnf clean packages'.
Error: Transaction test error:
file /usr/lib/.build-id/34/aac32bb4d3c0f44e72e57cf253a871240a1154 from install of ucsf-chimerax-1.2.5-1.el8.x86_64 conflicts with file from package rstudio-1.4.1106-1.x86_64
file /usr/lib/.build-id/80/916a3578c4abf8d9433986b7ca87ee58797eb5 from install of ucsf-chimerax-1.2.5-1.el8.x86_64 conflicts with file from package rstudio-1.4.1106-1.x86_64
file /usr/lib/.build-id/ea/6a2369dae8e186543b5e0fa413cb7ee7058c84 from install of ucsf-chimerax-1.2.5-1.el8.x86_64 conflicts with file from package rstudio-1.4.1106-1.x86_64
[murphy@eva02 Downloads]$ sudo dnf install ucsf-chimerax-1.2.5-1.el7.x86_64.rpm
Last metadata expiration check: 2:38:46 ago on Mon 31 May 2021 07:01:27 PM CDT.
Error:
Problem: conflicting requests
- nothing provides libgfortran4 needed by ucsf-chimerax-1.2.5-1.el7.x86_64
- nothing provides mesa-private-llvm needed by ucsf-chimerax-1.2.5-1.el7.x86_64
(try to add '--skip-broken' to skip uninstallable packages)
Update: ticket is here.
2nd Update: I installed it. Check the previous link. Had to remove
rstudio, installchimerax, and reinstallrstudio(but the one from the Fedora repositories).
VMD
vmd is another good alternative to pymol and it is free. Go here and download it, then do:
cd ~/Downloads
tar xvzf vmd-*tar.gz
cd vmd-VERSION/
./configure
cd src/
sudo make install
Where VERSION is the version of vmd.