thanks for the reply.
I am using Vista with 1.9.5, and I can now say that I have tested it in a different network, also with Vista and w7 and do not get any problems,
http://www.rcsb.org/pdb/files/3INS.pdb works fine in a browser but not in UGENE, so I guess as you pointed out it is indeed a network problem.
Have tried with and without using a proxy, and get the same results.
I also discovered today that the 'Check for updates' also gives a similar response
[Tasks][TRACE][10:53] releasing resource: 'Threads':1, state: 0/1000
[Tasks][TRACE][10:53] promoting task {Check for updates} to 'Finished', error 'Connection error: Connection refused (or timed out)'
[Tasks][ERROR][10:53] Task {Check for updates} finished with error: Connection error: Connection refused (or timed out)
[Tasks][TRACE][10:53] Unregistering task: Check for updates
[Tasks][TRACE][10:53] Deleting task: Check for updates
so everything seems to point towards a net problem rather than a UGENE one, I will try to sort it out and post back when I get it fixed,
thanks for the help,
Euan