another file ~/.local/share/applications/jna_jar.desktop
also need to be deleted. It seems to be openjdk brought by first time running pycharm.
[Desktop Entry]
Encoding=UTF-8
Version=1.0
Type=Application
Name=Welcome to PyCharm Community Edition
Icon=jna_jar.png
Exec=/usr/lib/jvm/java-7-openjdk-amd64/bin/java -Xbootclasspath/a:./../lib/boot.jar -classpath ./../lib/bootstrap.jar:./../lib/extensions.jar:./../lib/util.jar:./../lib/jdom.jar:./../lib/log4j.jar:./../lib/trove4j.jar:./../lib/jna.jar -Xms128m -Xmx750m -XX:MaxPermSize=350m -XX:ReservedCodeCacheSize=240m -XX:+UseConcMarkSweepGC -XX:SoftRefLRUPolicyMSPerMB=50 -ea -Dsun.io.useCanonCaches=false -Djava.net.preferIPv4Stack=true -XX:+HeapDumpOnOutOfMemoryError -XX:-OmitStackTraceInFastThrow -Dawt.useSystemAAFontSettings=lcd -Djb.vmOptionsFile=./pycharm64.vmoptions -XX:ErrorFile=/home/x/java_error_in_PYCHARM_%p.log -Djb.restart.code=88 -Didea.paths.selector=PyCharm50 -Didea.platform.prefix=PyCharmCore -Didea.no.jre.check=true com.intellij.idea.Main
StartupNotify=false
StartupWMClass=jetbrains-pycharm-ce
OnlyShowIn=Unity;
X-UnityGenerated=true
Several points done in the question was wrong.
1) Running sudo ls /usr/share/applications
with sudo is nonsense. Your user can read the data. How do
you think you get the icons in Dash? Think about it instead of wildly
adding sudo to commands when you don't get what you expect.
2) The files in /usr/share/applications define the files using
configuration lines in the files. The filename has no bearing here. You
could rename them all to random letters and numbers and Dash would still
work as it does now.
3) Try grep -i pycharm /usr/share/applications/*
to find out what should be deleted
sudo find / -type f -iname '*pycharm*'
– Raphael Jan 24 '16 at 9:46