If not create it (with sudo) and append it to the $PATH in your ~/.bash_profile. I think /usr/local/bin is in the default $PATH, check it by typing echo $PATH and looking for it. Do a symbolic link to somewhere in your $PATH with, for example: sudo ln -s /Applications/Chimera.app/Contents/MacOS/chimera /usr/local/bin/chimera.bash_profile with alias chimera = '/Applications/Chimera.app/Contents/MacOS/chimera' The binary is in /Applications/Chimera.app/Contents/MacOS/chimera. dmg file, drag Chimera icon to the Applications folder. This download is valid for the product(s) listed below. Check this by doing ls trajectories*.nc). Intel VMDenabled NVMe Driver for VMware ESXi Intel® Xeon® Scalable Family of Processors Intel® SSD Data Center PCIe NVMe See the release notes for installation instructions, supported hardware, what is new, bug fixes, and known issues. Now you’ll be able to load multiple trajectory filesįrom the command line like so: load_big_trajs.sh topology.prmtop trajectories*.nc (provided you have a sensible naming scheme of your trajectoriesĪnd they show up sequentially. If you’ve followed the previous steps it should be the same as the one in the script, though. Take a look at line 40 in the script and change the path to your VMD executable if it’s different! Applications/VMD1.9.2.app/Contents/Resources/VMD.app/Contents/MacOS/VMD -e $tmpfile -size 1920 1080 echo "mol new $prmtop " > $tmpfile for var in $ # We skip the first argument, the top file doĮcho "mol addfile $var first 0 step $stride waitfor all" > $tmpfile done # REPLACE THE PATH TO YOUR VMD EXECUTABLE! Or change the path to were its sitting in your machine. Prmtop = $1 tmpfile = $(mktemp /tmp/vmd_readin.tcl ) cat ~/Scripts/StateFile > $tmpfile # Comment this line out if you don't have a StateFile for VMD. Printf "Please provide at least two arguments (top and traj file) \n " printf "Usage: load_big_trajs.sh topology.prmtop trajectories*.nc \n " exit 1 # Usage: load_big_trajs.sh topology.prmtop trajectories*.nc if ] then The file in the /tmp/ directory is # removed after vmd is closed. # If it still fails (memory error), change the stride to # a bigger number. tcl file in the /tmp/ directory # with the necessary commands to call big trajectories # from the command line. Then make it an executable with chmod x load_big_trajs.sh. I’ve come up with a solution to this :heavy_exclamation_mark:Ĭopy or download the script below and save it somewhere in your Trajectories that are half the size of your RAM. This is bad because you’ll only be able to open NOTE: VMD only has 32-bit version for Mac OS X. Vmdappdir='/Applications/VMD1.9.2.app/Contents'Īlias vmd='"$vmdappdir/Resources/VMD.app/Contents/MacOS/VMD" $*' This is best done from the Finder (spaces in the command line are a pain to work with). Remove the space from the name of the Application (i.e. Navigating to wherever the files you want to visualize are. If you open VMD manually from the Dock it points every time to your home directory and you loose a lot of time manually Using VMD from the command line is very convenient as you can directly load the topology and trajectories files, or several PDBs Lower-left lock icon, and then select the Anywhere option under the Allow apps downloaded from: section. So you have to go to System Preferences > Security
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