<html><head></head><body style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space; ">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.<div><br></div><div>--Eric<br><div><div><br></div><div><span class="Apple-style-span" style="border-collapse: separate; -webkit-border-horizontal-spacing: 0px; -webkit-border-vertical-spacing: 0px; color: rgb(0, 0, 0); font-family: Helvetica; font-size: 16px; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: normal; -webkit-text-decorations-in-effect: none; text-indent: 0px; -webkit-text-size-adjust: auto; text-transform: none; orphans: 2; white-space: normal; widows: 2; word-spacing: 0px; "><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; "><font face="Helvetica" size="5" style="font: normal normal normal 16px/normal Helvetica; ">&nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp;&nbsp;Eric Pettersen</font></div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; "><font face="Helvetica" size="5" style="font: normal normal normal 16px/normal Helvetica; ">&nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp;&nbsp;UCSF Computer Graphics Lab</font></div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; "><font face="Helvetica" size="5" style="font: normal normal normal 16px/normal Helvetica; ">&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></font></div><br class="Apple-interchange-newline"></span></div><div>On Apr 4, 2013, at 11:22 AM, Tom Goddard wrote:</div><br class="Apple-interchange-newline"><blockquote type="cite">
  
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    <div class="moz-cite-prefix">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 class="moz-txt-link-rfc2396E" href="mailto:chris.wood@stfc.ac.uk">&lt;chris.wood@stfc.ac.uk&gt;</a><br>
      To: <a class="moz-txt-link-abbreviated" href="mailto:chimera-users@cgl.ucsf.edu">chimera-users@cgl.ucsf.edu</a><br>
      Date: 4/4/13 3:24 AM<br>
    </div>
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      <div class="WordSection1"><p class="MsoNormal">Hello,<o:p></o:p></p><p class="MsoNormal"><o:p>&nbsp;</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’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 lfo1">
          <!--[if !supportLists]--><span style="color:windowtext"><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></span><!--[endif]--><span style="color:windowtext">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<o:p></o:p></span></p><p class="MsoListParagraph" style="margin-left:20.25pt;text-indent:-18.0pt;mso-list:l0
          level1 lfo1">
          <!--[if !supportLists]--><span style="color:windowtext"><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></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 “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:p></o:p></span></p><p class="MsoListParagraph" style="margin-left:56.25pt;text-indent:-18.0pt;mso-list:l0
          level2 lfo1">
          <!--[if !supportLists]--><span style="font-family:&quot;Courier New&quot;;color:windowtext"><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;<o:p></o:p></span></p><p class="MsoNormal"><o:p>&nbsp;</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"><o:p>&nbsp;</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
          "C:\Program Files\Chimera 1.7\bin\lib\socket.py", 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"><o:p>&nbsp;</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"><o:p>&nbsp;</o:p></p><p class="MsoListParagraph" style="margin-left:54.0pt;text-indent:-18.0pt;mso-list:l1
          level1 lfo2">
          <!--[if !supportLists]--><span style="font-family:&quot;Courier New&quot;;color:windowtext"><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 “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. <o:p></o:p></span></p><p class="MsoNormal"><o:p>&nbsp;</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’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"><o:p>&nbsp;</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 style="color:black"><o:p></o:p></span></span></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<o:p></o:p></span></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<o:p></o:p></span></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<o:p></o:p></span></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<o:p></o:p></span></p><p class="MsoNormal"><span style="font-size:9.0pt;font-family:&quot;Verdana&quot;,&quot;sans-serif&quot;;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;;mso-fareast-language:EN-GB"><a moz-do-not-send="true" href="mailto:chris.wood@stfc.ac.uk">chris.wood@stfc.ac.uk</a><br>
            <a moz-do-not-send="true" href="http://www.ccpem.ac.uk/">www.ccpem.ac.uk</a><o:p></o:p></span></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: +44(0)1235 567864<o:p></o:p></span></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:
            +44(0)7909 586624<br>
            Fax: +44(0)1235 567801<o:p></o:p></span></p><p class="MsoNormal"><span style="font-size:9.0pt;font-family:&quot;Verdana&quot;,&quot;sans-serif&quot;;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;;mso-fareast-language:EN-GB">Skype:
            <a moz-do-not-send="true" href="callto://chris_c_wood/">chris_c_wood</a><o:p></o:p></span></p>
      </div>
      <br><p>-- <br>
        Scanned by iCritical.
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</pre>
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