You should probably be using 'CR/LF' as the terminator.
Do you want to collect 200 samples exactly, or do you want to collect 1 second's worth?
If you want 200 samples, then see http://www.mathworks.com/help/instrument/bytesavailablefcn.html -- set the bytesavailablefcncount to 200*6 and the mode to byte and set bytesavailablefcn to a routine that will fread() the 200*6 bytes, decode the sequences, store the data into a cumulative buffer if required, and plot the new data.
If you want 1 second's worth, set the bytesavailablefcncount to infinity, the mode to byte, and no bytesavailablefcn callback. Then create a timer() object that fires every 1 seconds. The timer routine should grab the bytesavailablecount (no 'fcn' in that name), and fread() that many bytes, decode the sequences, store the data into a cumulative buffer if required, and plot the new data.
Either way you should be sure to set the InputBufferSize to several times one second's-worth of data, so that data can be accumulating in the buffer while the callback is processing and plotting.
Note: it will be notably more overhead to attempt to read and process each packet as it comes in. Unless you need to control something in real time, try to read several samples at once.
Note: if your serial port is "serial over usb" then you are going to encounter additional timing constraints and might not be able to sample more than 50 Hz unless the driver on the far end is smart about sending the bytes over the USB.
