<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? 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.<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; "> 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; "> 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; "> <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>
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.<br>
<br>
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"><chris.wood@stfc.ac.uk></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> </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 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
"Times New Roman"">
</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
"Times New Roman"">
</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:"Courier New";color:windowtext"><span style="mso-list:Ignore">o<span style="font:7.0pt
"Times New Roman"">
</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: <o:p></o:p></span></p><p class="MsoNormal"><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"><o:p> </o:p></p><p class="MsoNormal"> File
"C:\Program Files\Chimera 1.7\bin\lib\socket.py", line 571, in
create_connection<o:p></o:p></p><p class="MsoNormal"> raise err<o:p></o:p></p><p class="MsoNormal"><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"><o:p> </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:"Courier New";color:windowtext"><span style="mso-list:Ignore">o<span style="font:7.0pt
"Times New Roman"">
</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> </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> </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:"Verdana","sans-serif";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:"Verdana","sans-serif";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:"Verdana","sans-serif";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:"Verdana","sans-serif";mso-fareast-language:EN-GB">Didcot<o:p></o:p></span></p><p class="MsoNormal"><span style="font-size:9.0pt;font-family:"Verdana","sans-serif";mso-fareast-language:EN-GB">OX11
0QX<o:p></o:p></span></p><p class="MsoNormal"><span style="font-size:9.0pt;font-family:"Verdana","sans-serif";mso-fareast-language:EN-GB"><o:p> </o:p></span></p><p class="MsoNormal"><span style="font-size:9.0pt;font-family:"Verdana","sans-serif";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:"Verdana","sans-serif";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:"Verdana","sans-serif";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:"Verdana","sans-serif";mso-fareast-language:EN-GB"><o:p> </o:p></span></p><p class="MsoNormal"><span style="font-size:9.0pt;font-family:"Verdana","sans-serif";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>
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