I'm afraid there is no ambiguity. You can't use the CCP4 version 6.* 
libraries in GPL software.

The approach adopted by Coot, which is GPL'd, is to use the CCP4 5.0.2 
libraries, which are LGPL, along with some patches currently maintained 
by Ralph Grosse-Kunstleve to address the more serious deficiencies of 
the older libraries.

Clipper comes under two different licences dependent on whether you get 
it from me or CCP4.

Kjeldgaard Morten wrote:
> Hi
> 
> The following excerpt from Richard Stallman's talk at the 5th 
> international GPLv3 conference 
> (http://www.fsfeurope.org/projects/gplv3/tokyo-rms-transcript) indicates 
> that there is a problem with the CCP4 license.
> 
> It is important to clarify this, and, as RMS says, that if you want to 
> make a more restrictive license, to do this in an unambiguous way.
> 
> It has major implications for those wanting to distribute their code 
> under the GPL (e.g. clipper, coot), but who also rely on code from the 
> CCP4, typically the library.
> 
> -- Morten
> 
> 
> 
> "While we were doing this [discussing GPLv3] we decided to try to put an 
> end to a misuse of the GPL. You may occasionally see a program which 
> says "This program is released under the GNU GPL but you're not allowed 
> to use it commercially", or some other attempt to add another 
> requirement. That's actually self-contradictory and its meaning is 
> ambiguous, so nobody can be sure what will happen if a judge looks at 
> that. After all, GPL version 2 says you can release a modified version 
> under GPL version 2. So if you take this program with its inconsistent 
> licence and you release a modified version, what licence are you 
> supposed to use? You could argue for two different possibilities."
> 
> "We can't stop people making their software under licences that are more 
> restrictive than the GPL, we can't stop them from releasing non-Free 
> Software, but we can try to prevent them from doing so in a misleading 
> and self-contradictory way, after all, when the program says GPL version 
> 2 but you can't use it commercially, that's not really released under 
> GPL version 2, and it's not Free Software, and if you tried to combine 
> that with code that really is released under GPL version 2, you would be 
> violating GPL2. Because this inconsistent licence starts out by saying 
> "GPL version 2", people are very likely to be mislead. They may think 
> it's available under GPL version 2, they may think they're allowed to 
> combine these modules. We want to get rid of this confusing practice. 
> And therefore we've stated that if you see a problem that states GPL 
> version 3 as its licence, but has additional requirements not explicitly 
> permitted in section 7 then you're entitled to remove them. We hope that 
> this will convince the people that want to use more restrictive licences 
> that they should do it in an unambiguous way. That is, they should take 
> the text, edit it, and make their own licence, which might be free or 
> might not, depending on the details, but at least it won't be the GNU 
> GPL, so people won't get confused."
> 
>