If you apply dictionary changes in single-user mode or if you use online schema changes, ProTop will not interfere and does not need to be stopped.
If the database is up in multi-user and you attempt to apply schema changes without the online-schema-changes flag, the ProTop agent, being a regular 4GL client, will prevent exclusive access to the database schema. In that case, you can pause ProTop using the following procedure:
1) Delete $PROTOP/tmp/*.flg. This will stop all ProTop processes (dbmonitor and pt3agents).
2) Stop the ProTop service, either by commenting out the dbmonitor cron job or stopping the Windows service
When you finish your schema changes, re-enable the ProTop service.