I need to calibrate my radio with a different antenna. I lost my instructions for calibration.

Check for a short in the Coax. Is the antenna near the cab of a truck or other body part? Is the antenna grounded? Has your radio been peeked and tuned?

tune your antenna not you radio. sounds like you don't have it grounded properly. new radio,new coax,and new antenna is the only way to do it right.make sure your antenna is at least 40" and it is adjustable with a set screw.

This is a common misunderstanding when it comes to communications equipment. You don't tune the antenna to the radio, but rather you tune the antenna to the vehicle. the vehicle is the ground plane for your antenna system.

With that said You will need an SWR Meter between your antenna and Radio. follow the instructions for your meter for calibrating the meter and follow the instructions for your antenna for adjusting the length.

VR5 tx power meter VR6 antenna warning light
There is not pot for swr cal internally. I guess the cal knob broad range pot or variable resistor. Swr readings after user calibration knob on front of radio, for meter should be close. Obviously not as good as external with larger scale meter. If you can not calibrate meter on face with this knob your radio may have less than 4 watts deadkey.
Just to be on the same page. Understand that SWR is a reading of antenna system condition or tuning of antenna to vehicle mounting location. This is a brief description.

Calibrate For SWR (Standing Wave Ratio) http://www.cbtricks.com/radios/cobra/29ltd_bt/graphics/cobra_29ltd_bt_om.pdf
The CAL is only to calibrate meter for a swr check of you antenna system it does not calibrate radio.

The CAL is to calibrate meter for reading SWR (standing wave ratio) which is reflected power when transmitting back to receiver(radio) from antenna system.
This CAL switch position when selected and mic keyed uses the CAL knob to align the meter needle with inverted red triangle next to cal on meter. Then when you select SWR switch position meter will display accurately when mic is keyed for that channel. Now notice the difference when you go between channels 1 and 40. The ant led light will act as idiot light if it is not lit then you are most likely safe to transmit.
I say system because your vehicle, antenna and coaxial cable are all part of this system. When you have a high reading and have to trim you antenna this is really calibrating the antenna to the vehicles body which acts as a ground plane.

The misconception is that you can calibrate a radio. You do not calibrate the radio. You tune the antenna. The calibrate knob on the radio is to calibrate the meter in it so you can check the SWR.

This article will tell you everything you need to know.

The calibrate knob only calibrates the radios SWR meter, the owners manual will show you the procedure for that. If your ANT light is coming on, it is telling you that your SWR is to high, and may cause damage to the radio from reflected power. You should purchase an in line meter as the radios internal meter may be somewhat unreliable. You need to tune the antenna to the lowest SWR possible. Typically anything under 2.0:1 is acceptable. Radio Shack sells a meter for about $50, and is pretty accurate. Antenna mounting can also cause high reflection if it is to close to other objects. Google "CB antenna tuning" or read the instruction manual for you antenna, and you should be able to figure out how to properly tune the antenna.

Changing the length of the mast more then likely made your antenna to short, and therefore impossible to tune.

You should not calibrate the antenna before you install it on the car!! the antenna needs to be calibrated on the vehicle that it is going to be on. Type of vehicle, different mounts, and many other variables can change the amount of reflection you will get.

j0hn9999 did a much better job but left some info out.

Take your SWR readings on channel 1, then on channel 40.... NOW, if your SWR is higher on ch 40 then ch 1, then your antenna is too long and it needs to be shortened. Refer to the antenna instructions on how to shorten the antenna.

If your SWR is higher on ch 1 then on ch 40 then your antenna is too short. You must lengthen the antenna. Again refer to your antenna instructions on how to lengthen your antenna.

You must calibrate each time you take a reading.

Make sure your doors and windows are shut when taking a reading

Make sure you are in an open lot when taking a reading as buildings, trees and other structures can cause reflection and give you an inaccurate reading.

If you adjust the length of your antenna on another vehicle and then put it on yours, the SWR will be off. It will need to be tuned again.

An external meter is better then the one in the radio, but will need to be hooked up in the vehicle you have the antenna on.

If you are not running any kind of power, or do not have a swing kit installed, and the radio is stock, the meter in the radio is more then enough to get a correct SWR reading.