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<p class="MsoNormal"><span style="font-size:9.0pt;font-family:&quot;Verdana&quot;,&quot;sans-serif&quot;;color:black;mso-fareast-language:EN-GB">Hi Tom / Eric,<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:9.0pt;font-family:&quot;Verdana&quot;,&quot;sans-serif&quot;;color:black;mso-fareast-language:EN-GB"><o:p>&nbsp;</o:p></span></p>
<p class="MsoNormal"><span style="font-size:9.0pt;font-family:&quot;Verdana&quot;,&quot;sans-serif&quot;;color:black;mso-fareast-language:EN-GB">Thanks for your replies.&nbsp; I suspected it would be a VirtualBox problem &#8211; it is fairly unstable (sometimes, an mrc file can be read,
 other times, opening the same file results in a fatal error as a result of OpenGL errors); e.g.<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:9.0pt;font-family:&quot;Verdana&quot;,&quot;sans-serif&quot;;color:black;mso-fareast-language:EN-GB"><o:p>&nbsp;</o:p></span></p>
<p class="MsoNormal"><span style="font-size:9.0pt;font-family:&quot;Verdana&quot;,&quot;sans-serif&quot;;color:black;mso-fareast-language:EN-GB">OpenGL error in GfxInfo::initialize 'invalid enumerant'<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:9.0pt;font-family:&quot;Verdana&quot;,&quot;sans-serif&quot;;color:black;mso-fareast-language:EN-GB">OpenGL error in GfxInfo::initialize 'invalid enumerant'<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:9.0pt;font-family:&quot;Verdana&quot;,&quot;sans-serif&quot;;color:black;mso-fareast-language:EN-GB">OpenGL error in GfxInfo::initialize 'invalid enumerant'<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:9.0pt;font-family:&quot;Verdana&quot;,&quot;sans-serif&quot;;color:black;mso-fareast-language:EN-GB">OpenGL Warning: glXChooseVisual: bad attrib=0x186a0, ignoring<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:9.0pt;font-family:&quot;Verdana&quot;,&quot;sans-serif&quot;;color:black;mso-fareast-language:EN-GB">OpenGL Warning: glXChooseVisual: bad attrib=0x186a1, ignoring<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:9.0pt;font-family:&quot;Verdana&quot;,&quot;sans-serif&quot;;color:black;mso-fareast-language:EN-GB">OpenGL Warning: No pincher, please call crStateSetCurrentPointers() in your SPU<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:9.0pt;font-family:&quot;Verdana&quot;,&quot;sans-serif&quot;;color:black;mso-fareast-language:EN-GB"><o:p>&nbsp;</o:p></span></p>
<p class="MsoNormal"><span style="font-size:9.0pt;font-family:&quot;Verdana&quot;,&quot;sans-serif&quot;;color:black;mso-fareast-language:EN-GB">To answer Eric&#8217;s question: if the Rapid Access Interface is shown, then I can see the menus; the Rapid Access Interface is the screen
 I see when I open chimera.&nbsp; If I then click on the lightening bolt to show a blank 3D window, then I can&#8217;t see the menus. Reverting back to the Rapid Acces Interface enables me to see the menus again.<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:9.0pt;font-family:&quot;Verdana&quot;,&quot;sans-serif&quot;;color:black;mso-fareast-language:EN-GB"><o:p>&nbsp;</o:p></span></p>
<p class="MsoNormal"><span style="font-size:9.0pt;font-family:&quot;Verdana&quot;,&quot;sans-serif&quot;;color:black;mso-fareast-language:EN-GB">Chris<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:9.0pt;font-family:&quot;Verdana&quot;,&quot;sans-serif&quot;;color:black;mso-fareast-language:EN-GB"><o:p>&nbsp;</o:p></span></p>
<p class="MsoNormal"><o:p>&nbsp;</o:p></p>
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<p class="MsoNormal"><b><span lang="EN-US" style="font-size:10.0pt;font-family:&quot;Tahoma&quot;,&quot;sans-serif&quot;;mso-fareast-language:EN-GB">From:</span></b><span lang="EN-US" style="font-size:10.0pt;font-family:&quot;Tahoma&quot;,&quot;sans-serif&quot;;mso-fareast-language:EN-GB"> Eric Pettersen
 [mailto:pett@cgl.ucsf.edu] <br>
<b>Sent:</b> 04 April 2013 19:29<br>
<b>To:</b> Tom Goddard<br>
<b>Cc:</b> Wood, Chris (STFC,RAL,SC); chimera-users@cgl.ucsf.edu<br>
<b>Subject:</b> Re: [Chimera-users] Proxy / graphics issues related to Virtual Box?<o:p></o:p></span></p>
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<p class="MsoNormal"><o:p>&nbsp;</o:p></p>
<p class="MsoNormal">Just out of curiosity, if the Rapid Access interface is showing instead of the 3D graphics window, can you see the menus? &nbsp;You can bring up Rapid Access with the lightning-bolt icon at the lower left of the Chimera window. &nbsp;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.<o:p></o:p></p>
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<p class="MsoNormal"><o:p>&nbsp;</o:p></p>
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<p class="MsoNormal">--Eric<o:p></o:p></p>
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<p class="MsoNormal"><o:p>&nbsp;</o:p></p>
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<p class="MsoNormal"><span style="font-family:&quot;Helvetica&quot;,&quot;sans-serif&quot;;color:black">&nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp;&nbsp;Eric Pettersen<o:p></o:p></span></p>
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<p class="MsoNormal"><span style="font-family:&quot;Helvetica&quot;,&quot;sans-serif&quot;;color:black">&nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp;&nbsp;UCSF Computer Graphics Lab<o:p></o:p></span></p>
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<p class="MsoNormal"><span style="font-family:&quot;Helvetica&quot;,&quot;sans-serif&quot;;color:black">&nbsp; &nbsp;&nbsp; &nbsp;&nbsp; &nbsp;&nbsp; &nbsp;&nbsp; &nbsp;&nbsp; &nbsp;&nbsp; &nbsp;&nbsp; &nbsp;<a href="http://www.cgl.ucsf.edu">http://www.cgl.ucsf.edu</a><o:p></o:p></span></p>
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<p class="MsoNormal"><span style="font-family:&quot;Helvetica&quot;,&quot;sans-serif&quot;;color:black"><br>
<br>
</span><span style="font-family:&quot;Times New Roman&quot;,&quot;serif&quot;"><o:p></o:p></span></p>
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<p class="MsoNormal">On Apr 4, 2013, at 11:22 AM, Tom Goddard wrote:<o:p></o:p></p>
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<br>
<o:p></o:p></p>
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<p class="MsoNormal">Hi Chris,<br>
<br>
&nbsp; Your problems are system configuration and Virtual Box bugs.&nbsp; Menus appearing behind the window -- is certainly a window system bug.&nbsp; Your fetching errors and chimera update errors are network connection problems.&nbsp; It doesn't look like any of this has to
 do with Chimera.<br>
<br>
&nbsp;&nbsp;&nbsp; Tom<br>
<br>
<br>
-------- Original Message --------<br>
Subject: [Chimera-users] Proxy / graphics issues related to Virtual Box?<br>
From: <a href="mailto:chris.wood@stfc.ac.uk">&lt;chris.wood@stfc.ac.uk&gt;</a><br>
To: <a href="mailto:chimera-users@cgl.ucsf.edu">chimera-users@cgl.ucsf.edu</a><br>
Date: 4/4/13 3:24 AM<o:p></o:p></p>
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<p class="MsoNormal">Hello,<o:p></o:p></p>
<p class="MsoNormal">&nbsp;<o:p></o:p></p>
<p class="MsoNormal">Having fixed my main problem issue of getting Chimera to run on a Virtual Box (see my previous email), I&#8217;ve got two quick questions which may or may not be as a result of running Chimera on a &nbsp;Virtual Box:<o:p></o:p></p>
<p class="MsoListParagraph" style="margin-left:20.25pt;text-indent:-18.0pt;mso-list:l0 level1 lfo2">
<![if !supportLists]><span style="mso-list:Ignore">-<span style="font:7.0pt &quot;Times New Roman&quot;">&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
</span></span><![endif]><span style="color:windowtext">When I have a structure open, I am unable to view any of the menus &#8211; 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</span><o:p></o:p></p>
<p class="MsoListParagraph" style="margin-left:20.25pt;text-indent:-18.0pt;mso-list:l0 level1 lfo2">
<![if !supportLists]><span style="mso-list:Ignore">-<span style="font:7.0pt &quot;Times New Roman&quot;">&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
</span></span><![endif]><span style="color:windowtext">In Ubuntu (my virtual OS), when I try and fetch a structure from the EMDB, I get an error message that &#8220;Error fetching EMDB 1048: [Errno ftp error] proxy support for ftp protocol currently not implemented&#8221;
 - although I assume that this is normal behaviour when trying to download files across a proxy?</span><o:p></o:p></p>
<p class="MsoListParagraph" style="margin-left:56.25pt;text-indent:-18.0pt;mso-list:l0 level2 lfo2">
<![if !supportLists]><span style="font-family:&quot;Courier New&quot;"><span style="mso-list:Ignore">o<span style="font:7.0pt &quot;Times New Roman&quot;">&nbsp;&nbsp;
</span></span></span><![endif]><span style="color:windowtext">However, in Windows (my host OS) I get a different error when trying to fetch the same structure: &nbsp;</span><o:p></o:p></p>
<p class="MsoNormal">&nbsp;<o:p></o:p></p>
<p class="MsoNormal" style="text-indent:36.0pt">error: [Errno 10061] No connection could be made because the target machine actively refused it<o:p></o:p></p>
<p class="MsoNormal">&nbsp;<o:p></o:p></p>
<p class="MsoNormal">&nbsp; &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; File &quot;C:\Program Files\Chimera 1.7\bin\lib\socket.py&quot;, line 571, in create_connection<o:p></o:p></p>
<p class="MsoNormal">&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; raise err<o:p></o:p></p>
<p class="MsoNormal">&nbsp;<o:p></o:p></p>
<p class="MsoNormal" style="margin-left:36.0pt;text-indent:36.0pt">See reply log for Python traceback.<o:p></o:p></p>
<p class="MsoNormal">&nbsp;<o:p></o:p></p>
<p class="MsoListParagraph" style="margin-left:54.0pt;text-indent:-18.0pt;mso-list:l1 level1 lfo4">
<![if !supportLists]><span style="font-family:&quot;Courier New&quot;"><span style="mso-list:Ignore">o<span style="font:7.0pt &quot;Times New Roman&quot;">&nbsp;&nbsp;
</span></span></span><![endif]><span style="color:windowtext">When I use the &#8220;Check for updates&#8221; 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: &#8220;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.&#8221; &#8211; although I do have
 the proxy server set in Network Places. </span><o:p></o:p></p>
<p class="MsoNormal">&nbsp;<o:p></o:p></p>
<p class="MsoNormal">Although these are relatively minor bugs, I thought you might like to be made aware of them (if you weren&#8217;t already!), or that you might know how I could fix them, if they are problems to do with my setup!<o:p></o:p></p>
<p class="MsoNormal">&nbsp;<o:p></o:p></p>
<p class="MsoNormal">Cheers,<o:p></o:p></p>
<p class="MsoNormal">Chris<o:p></o:p></p>
<p class="MsoNormal"><span style="font-size:9.0pt;font-family:&quot;Verdana&quot;,&quot;sans-serif&quot;;mso-fareast-language:EN-GB">-------------------</span><o:p></o:p></p>
<p class="MsoNormal"><span style="font-size:9.0pt;font-family:&quot;Verdana&quot;,&quot;sans-serif&quot;;mso-fareast-language:EN-GB">Dr Chris Wood</span><o:p></o:p></p>
<p class="MsoNormal"><span style="font-size:9.0pt;font-family:&quot;Verdana&quot;,&quot;sans-serif&quot;;mso-fareast-language:EN-GB">STFC Rutherford Appleton Laboratory</span><o:p></o:p></p>
<p class="MsoNormal"><span style="font-size:9.0pt;font-family:&quot;Verdana&quot;,&quot;sans-serif&quot;;mso-fareast-language:EN-GB">Didcot</span><o:p></o:p></p>
<p class="MsoNormal"><span style="font-size:9.0pt;font-family:&quot;Verdana&quot;,&quot;sans-serif&quot;;mso-fareast-language:EN-GB">OX11 0QX</span><o:p></o:p></p>
<p class="MsoNormal"><span style="font-size:9.0pt;font-family:&quot;Verdana&quot;,&quot;sans-serif&quot;;mso-fareast-language:EN-GB">&nbsp;</span><o:p></o:p></p>
<p class="MsoNormal"><span style="font-size:9.0pt;font-family:&quot;Verdana&quot;,&quot;sans-serif&quot;;mso-fareast-language:EN-GB"><a href="mailto:chris.wood@stfc.ac.uk">chris.wood@stfc.ac.uk</a><br>
<a href="http://www.ccpem.ac.uk/">www.ccpem.ac.uk</a></span><o:p></o:p></p>
<p class="MsoNormal"><span style="font-size:9.0pt;font-family:&quot;Verdana&quot;,&quot;sans-serif&quot;;mso-fareast-language:EN-GB"><br>
Tel: &#43;44(0)1235 567864</span><o:p></o:p></p>
<p class="MsoNormal"><span style="font-size:9.0pt;font-family:&quot;Verdana&quot;,&quot;sans-serif&quot;;mso-fareast-language:EN-GB">Tel: &#43;44(0)7909 586624<br>
Fax: &#43;44(0)1235 567801</span><o:p></o:p></p>
<p class="MsoNormal"><span style="font-size:9.0pt;font-family:&quot;Verdana&quot;,&quot;sans-serif&quot;;mso-fareast-language:EN-GB">&nbsp;</span><o:p></o:p></p>
<p class="MsoNormal"><span style="font-size:9.0pt;font-family:&quot;Verdana&quot;,&quot;sans-serif&quot;;mso-fareast-language:EN-GB">Skype:
<a href="callto://chris_c_wood/">chris_c_wood</a></span><o:p></o:p></p>
<p class="MsoNormal"><span style="font-size:12.0pt;font-family:&quot;Times New Roman&quot;,&quot;serif&quot;;mso-fareast-language:EN-GB"><o:p>&nbsp;</o:p></span></p>
<p>-- <br>
Scanned by iCritical. <o:p></o:p></p>
<p class="MsoNormal"><span style="font-size:12.0pt;font-family:&quot;Times New Roman&quot;,&quot;serif&quot;;mso-fareast-language:EN-GB"><br>
<br>
<br>
<br>
<o:p></o:p></span></p>
<pre>_______________________________________________<o:p></o:p></pre>
<pre>Chimera-users mailing list<o:p></o:p></pre>
<pre><a href="mailto:Chimera-users@cgl.ucsf.edu">Chimera-users@cgl.ucsf.edu</a><o:p></o:p></pre>
<pre><a href="http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users">http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users</a><o:p></o:p></pre>
</blockquote>
<p class="MsoNormal"><span style="font-size:12.0pt;font-family:&quot;Times New Roman&quot;,&quot;serif&quot;;mso-fareast-language:EN-GB"><o:p>&nbsp;</o:p></span></p>
</div>
<p class="MsoNormal"><span style="font-size:12.0pt;font-family:&quot;Times New Roman&quot;,&quot;serif&quot;;mso-fareast-language:EN-GB">_______________________________________________<br>
Chimera-users mailing list<br>
<a href="mailto:Chimera-users@cgl.ucsf.edu">Chimera-users@cgl.ucsf.edu</a><br>
<a href="http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users">http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users</a><o:p></o:p></span></p>
</div>
<p class="MsoNormal"><span style="font-size:12.0pt;font-family:&quot;Times New Roman&quot;,&quot;serif&quot;;mso-fareast-language:EN-GB"><o:p>&nbsp;</o:p></span></p>
</div>
<p class="MsoNormal" style="margin-bottom:12.0pt"><span style="font-size:12.0pt;font-family:&quot;Times New Roman&quot;,&quot;serif&quot;;mso-fareast-language:EN-GB"><o:p>&nbsp;</o:p></span></p>
</div>

<br><p>-- 
<BR>Scanned by iCritical.
</p>
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