The pem certificate needs to be converted and split into two files (public and private key). I think the information on the following page will help:
http://digitalpbk.blogspot.de/2011/10/convert-amazon-ec2-pem-files-to-ppk.htmlYou need to save both the public key and the private key on your hard disk.
Once you have your separate key files, here are some generic steps for configuring a client certificate.
1. FTP DIALOG, FIRST TAB SHEET
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Enter User ID but no password.
Save User ID (checked)
2. CERTIFICATES TAB SHEET
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Name: My Certificate (for example)
Certificate/Private Key File: C:\Users\Tobias\Documents\myprivatekeyfile
Public Key File: C:\Users\Tobias\Documents\mypublickeyfile.pub
***** NOW CLICK ADD BUTTON *****
3. SECURITY TAB SHEET
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Choose the certificate from the drop-down menu in the lower right
half of the dialog. Specify the password for the file.
Remove "User Name / Password"
If problems remain, please make sure you have the latest version of the software.