carma v.2.3 released.

[Nicholas M. Glykos]

Dear All,

A new stable version (v.2.3) of carma & friends has been released and is
available for download from carma's homepage or github.

This is mostly a bug-fixing release with one addition : carma can now
calculate and emit the accessible surface area of a protein component as a
function of simulation time. The calculation of ASA is performed
automatically whenever you use the '-stride' flag to calculate secondary
structure. A typical command for a single-chain protein would have been :

carma -v -w -pdb -stride -segid A -atmid HEAVY my.dcd my.psf

The ASA estimates are written in the file 'carma.ASA.dat'. The graph of
'ASA vs. Frame' can also be produced and viewed and saved as a postscript
file through grcarma :

grcarma => Secondary structure => View results => surface.ASA.*.dat



Kind regards,
Nicholas


__________________________________________________________________________

New quick installation instructions for Linux machines
__________________________________________________________________________

From a terminal (unix shell) give

wget https://utopia.duth.gr/glykos/progs/carma.v.2.3.run
chmod 755 carma.v.2.3.run
./carma.v.2.3.run

This will install everything in /usr/local/ including carma, grcarma,
stride, cluster5D & cwords. You may need root privileges for the last
command to work (use "sudo ./carma.v.2.3.run"). For 5D clustering and
weblogo diagrams to work you need to install tcsh & weblogo (sudo apt
install tcsh ; pip3 install weblogo).





--


Nicholas M. Glykos, Department of Molecular Biology
and Genetics, Democritus University of Thrace, University Campus,
Dragana, 68100 Alexandroupolis, Greece, Tel/Fax (office) +302551030620,
Ext.77620, Tel (lab) +302551030615, https://utopia.duth.gr/glykos/