<html xmlns:v="urn:schemas-microsoft-com:vml" xmlns:o="urn:schemas-microsoft-com:office:office" xmlns:w="urn:schemas-microsoft-com:office:word" xmlns:m="http://schemas.microsoft.com/office/2004/12/omml" xmlns="http://www.w3.org/TR/REC-html40">
<head>
<meta http-equiv="Content-Type" content="text/html; charset=us-ascii">
<meta name="Generator" content="Microsoft Word 14 (filtered medium)">
<style><!--
/* Font Definitions */
@font-face
{font-family:Wingdings;
panose-1:5 0 0 0 0 0 0 0 0 0;}
@font-face
{font-family:Wingdings;
panose-1:5 0 0 0 0 0 0 0 0 0;}
@font-face
{font-family:Calibri;
panose-1:2 15 5 2 2 2 4 3 2 4;}
@font-face
{font-family:Verdana;
panose-1:2 11 6 4 3 5 4 4 2 4;}
/* Style Definitions */
p.MsoNormal, li.MsoNormal, div.MsoNormal
{margin:0cm;
margin-bottom:.0001pt;
font-size:11.0pt;
font-family:"Calibri","sans-serif";
mso-fareast-language:EN-US;}
a:link, span.MsoHyperlink
{mso-style-priority:99;
color:blue;
text-decoration:underline;}
a:visited, span.MsoHyperlinkFollowed
{mso-style-priority:99;
color:purple;
text-decoration:underline;}
p.MsoListParagraph, li.MsoListParagraph, div.MsoListParagraph
{mso-style-priority:34;
margin-top:0cm;
margin-right:0cm;
margin-bottom:0cm;
margin-left:36.0pt;
margin-bottom:.0001pt;
font-size:11.0pt;
font-family:"Calibri","sans-serif";
color:black;
mso-fareast-language:EN-US;}
span.EmailStyle17
{mso-style-type:personal-compose;
font-family:"Calibri","sans-serif";
color:windowtext;}
.MsoChpDefault
{mso-style-type:export-only;
font-family:"Calibri","sans-serif";
mso-fareast-language:EN-US;}
@page WordSection1
{size:612.0pt 792.0pt;
margin:72.0pt 72.0pt 72.0pt 72.0pt;}
div.WordSection1
{page:WordSection1;}
/* List Definitions */
@list l0
{mso-list-id:219170363;
mso-list-type:hybrid;
mso-list-template-ids:-1868263052 1188492424 134807555 134807557 134807553 134807555 134807557 134807553 134807555 134807557;}
@list l0:level1
{mso-level-start-at:0;
mso-level-number-format:bullet;
mso-level-text:-;
mso-level-tab-stop:none;
mso-level-number-position:left;
margin-left:20.25pt;
text-indent:-18.0pt;
font-family:"Calibri","sans-serif";
mso-fareast-font-family:Calibri;}
@list l0:level2
{mso-level-number-format:bullet;
mso-level-text:o;
mso-level-tab-stop:none;
mso-level-number-position:left;
margin-left:56.25pt;
text-indent:-18.0pt;
font-family:"Courier New";}
@list l0:level3
{mso-level-number-format:bullet;
mso-level-text:\F0A7;
mso-level-tab-stop:none;
mso-level-number-position:left;
margin-left:92.25pt;
text-indent:-18.0pt;
font-family:Wingdings;}
@list l0:level4
{mso-level-number-format:bullet;
mso-level-text:\F0B7;
mso-level-tab-stop:none;
mso-level-number-position:left;
margin-left:128.25pt;
text-indent:-18.0pt;
font-family:Symbol;}
@list l0:level5
{mso-level-number-format:bullet;
mso-level-text:o;
mso-level-tab-stop:none;
mso-level-number-position:left;
margin-left:164.25pt;
text-indent:-18.0pt;
font-family:"Courier New";}
@list l0:level6
{mso-level-number-format:bullet;
mso-level-text:\F0A7;
mso-level-tab-stop:none;
mso-level-number-position:left;
margin-left:200.25pt;
text-indent:-18.0pt;
font-family:Wingdings;}
@list l0:level7
{mso-level-number-format:bullet;
mso-level-text:\F0B7;
mso-level-tab-stop:none;
mso-level-number-position:left;
margin-left:236.25pt;
text-indent:-18.0pt;
font-family:Symbol;}
@list l0:level8
{mso-level-number-format:bullet;
mso-level-text:o;
mso-level-tab-stop:none;
mso-level-number-position:left;
margin-left:272.25pt;
text-indent:-18.0pt;
font-family:"Courier New";}
@list l0:level9
{mso-level-number-format:bullet;
mso-level-text:\F0A7;
mso-level-tab-stop:none;
mso-level-number-position:left;
margin-left:308.25pt;
text-indent:-18.0pt;
font-family:Wingdings;}
@list l1
{mso-list-id:688019952;
mso-list-type:hybrid;
mso-list-template-ids:-1578569600 134807555 134807577 134807579 134807567 134807577 134807579 134807567 134807577 134807579;}
@list l1:level1
{mso-level-number-format:bullet;
mso-level-text:o;
mso-level-tab-stop:none;
mso-level-number-position:left;
margin-left:54.0pt;
text-indent:-18.0pt;
font-family:"Courier New";}
@list l1:level2
{mso-level-number-format:alpha-lower;
mso-level-tab-stop:none;
mso-level-number-position:left;
margin-left:90.0pt;
text-indent:-18.0pt;}
@list l1:level3
{mso-level-number-format:roman-lower;
mso-level-tab-stop:none;
mso-level-number-position:right;
margin-left:126.0pt;
text-indent:-9.0pt;}
@list l1:level4
{mso-level-tab-stop:none;
mso-level-number-position:left;
margin-left:162.0pt;
text-indent:-18.0pt;}
@list l1:level5
{mso-level-number-format:alpha-lower;
mso-level-tab-stop:none;
mso-level-number-position:left;
margin-left:198.0pt;
text-indent:-18.0pt;}
@list l1:level6
{mso-level-number-format:roman-lower;
mso-level-tab-stop:none;
mso-level-number-position:right;
margin-left:234.0pt;
text-indent:-9.0pt;}
@list l1:level7
{mso-level-tab-stop:none;
mso-level-number-position:left;
margin-left:270.0pt;
text-indent:-18.0pt;}
@list l1:level8
{mso-level-number-format:alpha-lower;
mso-level-tab-stop:none;
mso-level-number-position:left;
margin-left:306.0pt;
text-indent:-18.0pt;}
@list l1:level9
{mso-level-number-format:roman-lower;
mso-level-tab-stop:none;
mso-level-number-position:right;
margin-left:342.0pt;
text-indent:-9.0pt;}
ol
{margin-bottom:0cm;}
ul
{margin-bottom:0cm;}
--></style><!--[if gte mso 9]><xml>
<o:shapedefaults v:ext="edit" spidmax="1026" />
</xml><![endif]--><!--[if gte mso 9]><xml>
<o:shapelayout v:ext="edit">
<o:idmap v:ext="edit" data="1" />
</o:shapelayout></xml><![endif]-->
</head>
<body lang="EN-GB" link="blue" vlink="purple">
<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 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><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 href="callto://chris_c_wood/">chris_c_wood</a><o:p></o:p></span></p>
</div>
<br><p>--
<BR>Scanned by iCritical.
</p>
<br></body>
</html>