[Chimera-users] Proxy / graphics issues related to Virtual Box?

Eric Pettersen pett at cgl.ucsf.edu
Thu Apr 4 11:29:18 PDT 2013

Just out of curiosity, if the Rapid Access interface is showing instead of the 3D graphics window, can you see the menus?  You can bring up Rapid Access with the lightning-bolt icon at the lower left of the Chimera window.  Not that I have a solution if the menus do show in that case, but just that it would indicate that the Virtual Box bug is related to showing menus over 3D graphics contexts.


                        Eric Pettersen
                        UCSF Computer Graphics Lab

On Apr 4, 2013, at 11:22 AM, Tom Goddard wrote:

> Hi Chris,
>   Your problems are system configuration and Virtual Box bugs.  Menus appearing behind the window -- is certainly a window system bug.  Your fetching errors and chimera update errors are network connection problems.  It doesn't look like any of this has to do with Chimera.
>     Tom
> -------- Original Message --------
> Subject: [Chimera-users] Proxy / graphics issues related to Virtual Box?
> From: <chris.wood at stfc.ac.uk>
> To: chimera-users at cgl.ucsf.edu
> Date: 4/4/13 3:24 AM
>> Hello,
>> Having fixed my main problem issue of getting Chimera to run on a Virtual Box (see my previous email), I’ve got two quick questions which may or may not be as a result of running Chimera on a  Virtual Box:
>> -          When I have a structure open, I am unable to view any of the menus – when I click on a menu title, I can just see that the menus do open, but are below / behind the black canvas background (the closest analogy I can think of is that the z-index, the terminology used in CSS/HTML for determining which objects appear infront of other ones) appears to be incorrect
>> -          In Ubuntu (my virtual OS), when I try and fetch a structure from the EMDB, I get an error message that “Error fetching EMDB 1048: [Errno ftp error] proxy support for ftp protocol currently not implemented” - although I assume that this is normal behaviour when trying to download files across a proxy?
>> o   However, in Windows (my host OS) I get a different error when trying to fetch the same structure:  
>> error: [Errno 10061] No connection could be made because the target machine actively refused it
>>                                 File "C:\Program Files\Chimera 1.7\bin\lib\socket.py", line 571, in create_connection
>>                                 raise err
>> See reply log for Python traceback.
>> o   When I use the “Check for updates” button in the Ubuntu version, it gives me a message that I am running chimera candidate 1.7, and that there is a newer version available, but when I click the same button in Windows, I get an error: “Unable to contact UCSF Computer Graphics Lab to check for new version. Either the network connection is down somewhere in between or an HTTP proxy needs to be configured with the Web Access preference.” – although I do have the proxy server set in Network Places.
>> Although these are relatively minor bugs, I thought you might like to be made aware of them (if you weren’t already!), or that you might know how I could fix them, if they are problems to do with my setup!
>> Cheers,
>> Chris
>> -------------------
>> Dr Chris Wood
>> STFC Rutherford Appleton Laboratory
>> Didcot
>> OX11 0QX
>> chris.wood at stfc.ac.uk
>> www.ccpem.ac.uk
>> Tel: +44(0)1235 567864
>> Tel: +44(0)7909 586624
>> Fax: +44(0)1235 567801
>> Skype: chris_c_wood
>> -- 
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