htaccess issues

Hello
I just updated WP to the latest version and now only the site’s homepage is functioning and all the PERMAlinks are not showing: mistresselektra.com

I did notice the htaccess file contained no data so I inserted code like this:

# BEGIN WordPress
<IfModule mod_rewrite.c>
RewriteEngine On
RewriteBase /wordpress/
RewriteRule ^index\.php$ - [L]
RewriteCond %{REQUEST_FILENAME} !-f
RewriteCond %{REQUEST_FILENAME} !-d
RewriteRule . /wordpress/index.php [L]
</IfModule>

# END WordPress

[ Please use the backtick ` or code button for code. It makes it much more readable. ]

Am I suppose to manually add in all the permalinks? Is it a file permission error?
Any ideas anyone?
Also…I HAD malware on my site but it was cleaned off…
Thank you
Morpheus