How To Install dssp on CentOS 8
Introduction
In this tutorial we learn how to install dssp on CentOS 8.
What is dssp
The DSSP program standardizes protein secondary structure assignment. DSSP is a database of secondary structure assignments (and much more) for all protein entries in the Protein Data Bank (PDB). DSSP is also the program that calculates DSSP entries from PDB entries. DSSP does not predict secondary structure. References “A series of PDB related databases for everyday needs.”, Robbie P. Joosten, Tim A.H. te Beek, Elmar Krieger, Maarten L. Hekkelman, Rob W.W. Hooft, Reinhard Schneider, Chris Sander, and Gert Vriend. Nucleic Acids Research 2011 January; 39(Database issue) doi “Dictionary of protein secondary structure hydrogen-bonded and geometrical features.”, Kabsch W, Sander C, Biopolymers. 1983 22 2577-2637.
We can use yum or dnf to install dssp on CentOS 8. In this tutorial we discuss both methods but you only need to choose one of method to install dssp.
Install dssp on CentOS 8 Using dnf
Update yum database with dnf using the following command.
sudo dnf makecache --refresh
The output should look something like this:
CentOS Linux 8 - AppStream 43 kB/s | 4.3 kB 00:00
CentOS Linux 8 - BaseOS 65 kB/s | 3.9 kB 00:00
CentOS Linux 8 - ContinuousRelease 43 kB/s | 3.0 kB 00:00
CentOS Linux 8 - Extras 23 kB/s | 1.5 kB 00:00
CentOS Linux 8 - FastTrack 40 kB/s | 3.0 kB 00:00
CentOS Linux 8 - HighAvailability 36 kB/s | 3.9 kB 00:00
CentOS Linux 8 - Plus 24 kB/s | 1.5 kB 00:00
CentOS Linux 8 - PowerTools 50 kB/s | 4.3 kB 00:00
Extra Packages for Enterprise Linux Modular 8 - x86_64 13 kB/s | 9.2 kB 00:00
Extra Packages for Enterprise Linux 8 - x86_64 24 kB/s | 8.5 kB 00:00
Metadata cache created.
After updating yum database, We can install dssp using dnf by running the following command:
sudo dnf -y install dssp
Install dssp on CentOS 8 Using yum
Update yum database with yum using the following command.
sudo yum makecache --refresh
The output should look something like this:
CentOS Linux 8 - AppStream 43 kB/s | 4.3 kB 00:00
CentOS Linux 8 - BaseOS 65 kB/s | 3.9 kB 00:00
CentOS Linux 8 - ContinuousRelease 43 kB/s | 3.0 kB 00:00
CentOS Linux 8 - Extras 23 kB/s | 1.5 kB 00:00
CentOS Linux 8 - FastTrack 40 kB/s | 3.0 kB 00:00
CentOS Linux 8 - HighAvailability 36 kB/s | 3.9 kB 00:00
CentOS Linux 8 - Plus 24 kB/s | 1.5 kB 00:00
CentOS Linux 8 - PowerTools 50 kB/s | 4.3 kB 00:00
Extra Packages for Enterprise Linux Modular 8 - x86_64 13 kB/s | 9.2 kB 00:00
Extra Packages for Enterprise Linux 8 - x86_64 24 kB/s | 8.5 kB 00:00
Metadata cache created.
After updating yum database, We can install dssp using yum by running the following command:
sudo yum -y install dssp
How To Uninstall dssp on CentOS 8
To uninstall only the dssp package we can use the following command:
sudo dnf remove dssp
dssp Package Contents on CentOS 8
/usr/bin/mkdssp
/usr/lib/.build-id
/usr/lib/.build-id/cb
/usr/lib/.build-id/cb/aa2655c505d666c9a3458326fb62c04acd9b2a
/usr/share/doc/dssp
/usr/share/doc/dssp/README.txt
/usr/share/doc/dssp/changelog
/usr/share/licenses/dssp
/usr/share/licenses/dssp/LICENSE_1_0.txt
/usr/share/man/man1/mkdssp.1.gz
References
Summary
In this tutorial we learn how to install dssp on CentOS 8 using yum and dnf.
