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I got a MacBook Pro that has a problem booting, or even seeing the hard drive. I have used the recovery console to install OS X onto a USB drive and have booted into that and can't actually see the internal disk at all.

If I boot to Recovery Mode and open Disk Utility I can see it fine in there, and can see the files on it. If I check the disk using the repair option it also verifies fine.

If I take the drive out and put it in a USB caddy I can pull off all the files just fine using HSFExplorer on a PC, and have backed up most to an external drive from the PC. I can't quite work out why the Mac won't boot though as according to Disk Utility it's fine, but from inside OS X it cannot be seen, and also booting off it gives a question mark.

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The question mark means that it cannot find its boot partition. On any OS X drive, you are going to have several partitions. It might look something like:

 #:                       TYPE NAME                    SIZE       IDENTIFIER
   0:     Apple_partition_scheme                        *55.9 Gi    disk0
   1:        Apple_partition_map                         31.5 Ki    disk0s1
   2:                 Apple_Boot Boot OSX                128.0 Mi   disk0s2
   3:                 Apple_HFSX Macintosh HD0           25.0 Gi    disk0s3
   4:                 Apple_Boot                         128.0 Mi   disk0s4

Using this drive as an example, you can probably see what is on "Macintosh HD0" which is disk0s3. To boot, you need the "Apple_Boot" partition or disk0s4 partition.

You should be able to fix this by running the installer and having it repair the OS X installation.

Make sure you back up your files first (it sounds like you did).

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    Thanks, if I run the installer I still cant see the disk, only in disk utility of in os x itself when running of usb flash drive. – Iain Simpson Mar 12 '16 at 13:43
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    If you run installer, look at the top of the screen and you should see the "top bar" Under "Tools" is disk utility. You can run that one. – Allan Mar 12 '16 at 15:30
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This turned out to be the hard drive cable, once I replaced that it was back to working as normal.

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