<html>
<head>
<meta http-equiv="Content-Type" content="text/html; charset=Windows-1252">
<style type="text/css" style="display:none;"><!-- P {margin-top:0;margin-bottom:0;} --></style>
</head>
<body dir="ltr">
<div id="divtagdefaultwrapper" style="font-size:12pt;color:#000000;font-family:Calibri,Helvetica,sans-serif;" dir="ltr">
<p style="margin-top:0;margin-bottom:0">Hi Elaine,</p>
<p style="margin-top:0;margin-bottom:0"><br>
</p>
<p style="margin-top:0;margin-bottom:0">That's strange in that case. I still receive this error (and I reinstalled the latest stable version of Chimera today too).</p>
<p style="margin-top:0;margin-bottom:0"><br>
</p>
<p style="margin-top:0;margin-bottom:0">I'm familiar with this type of Python error, but not sure what it means in the context of not being able to communicate with the servers.</p>
<p style="margin-top:0;margin-bottom:0"><br>
</p>
<p style="margin-top:0;margin-bottom:0">The error:</p>
<p style="margin-top:0;margin-bottom:0">ValueError: Too make values to unpack</p>
<p style="margin-top:0;margin-bottom:0"><br>
</p>
<p style="margin-top:0;margin-bottom:0">File "/Applications/Chimera.app/Contents/Resources/share/AlignChains/gui.py, line 109, in __init__</p>
<p style="margin-top:0;margin-bottom:0"> serviceName, inOutFlags, serviceOptions = serviceinfo</p>
<p style="margin-top:0;margin-bottom:0"><br>
</p>
<p style="margin-top:0;margin-bottom:0"><br>
</p>
<p style="margin-top:0;margin-bottom:0"><br>
</p>
<div id="Signature">
<div id="divtagdefaultwrapper" dir="ltr" style="font-size: 12pt; color: rgb(0, 0, 0); font-family: Calibri, Arial, Helvetica, sans-serif, Helvetica, EmojiFont, "Apple Color Emoji", "Segoe UI Emoji", NotoColorEmoji, "Segoe UI Symbol", "Android Emoji", EmojiSymbols;">
<div id="divtagdefaultwrapper" style="font-size: 12pt; color: rgb(0, 0, 0); background-color: rgb(255, 255, 255); font-family: Calibri, Arial, Helvetica, sans-serif, Helvetica, EmojiFont, "Apple Color Emoji", "Segoe UI Emoji", NotoColorEmoji, "Segoe UI Symbol", "Android Emoji", EmojiSymbols;">
Joe Healey<br style="font-size:10pt">
</div>
<div id="divtagdefaultwrapper" style="font-size: 12pt; color: rgb(0, 0, 0); background-color: rgb(255, 255, 255); font-family: Calibri, Arial, Helvetica, sans-serif, Helvetica, EmojiFont, "Apple Color Emoji", "Segoe UI Emoji", NotoColorEmoji, "Segoe UI Symbol", "Android Emoji", EmojiSymbols;">
<br>
</div>
<div id="divtagdefaultwrapper" style="font-size: 12pt; color: rgb(0, 0, 0); background-color: rgb(255, 255, 255); font-family: Calibri, Arial, Helvetica, sans-serif, Helvetica, EmojiFont, "Apple Color Emoji", "Segoe UI Emoji", NotoColorEmoji, "Segoe UI Symbol", "Android Emoji", EmojiSymbols;">
<span style="text-decoration:underline"> </span><br>
</div>
<div id="divtagdefaultwrapper" style="font-size: 12pt; color: rgb(0, 0, 0); background-color: rgb(255, 255, 255); font-family: Calibri, Arial, Helvetica, sans-serif, Helvetica, EmojiFont, "Apple Color Emoji", "Segoe UI Emoji", NotoColorEmoji, "Segoe UI Symbol", "Android Emoji", EmojiSymbols;">
<span style="font-size:10pt">M.Sc. B.Sc. (Hons) MRSB</span><br>
</div>
<div id="divtagdefaultwrapper" style="font-size: 12pt; color: rgb(0, 0, 0); background-color: rgb(255, 255, 255); font-family: Calibri, Arial, Helvetica, sans-serif, Helvetica, EmojiFont, "Apple Color Emoji", "Segoe UI Emoji", NotoColorEmoji, "Segoe UI Symbol", "Android Emoji", EmojiSymbols;">
<span style="font-size:10pt"></span>
<div><span style="font-size:10pt">PhD Student</span></div>
<div><span style="font-size:10pt">MOAC CDT, Senate House</span></div>
<div><span style="font-size:10pt">University of Warwick<br style="">
</span></div>
<div><span style="font-size:10pt">Coventry<br style="">
</span></div>
<div><span style="font-size:10pt">CV47AL<br style="">
Mob: +44 (0) 7536 042620 | </span><span style="font-size:10pt">Email: J.R.J.Healey@warwick.ac.uk</span></div>
<div><span style="font-size:10pt"><br style="">
</span></div>
<div><span style="font-size:10pt">Jointly working in:<br style="">
</span></div>
<div><span style="font-size:10pt"><a href="http://www2.warwick.ac.uk/fac/med/research/tsm/microinfect/staff/waterfieldlab/" id="LPNoLP">Waterfield Lab</a> (<span style="font-family:Calibri,Arial,Helvetica,sans-serif; font-size:13.3333330154419px; background-color:rgb(255,255,255)">WMS </span><span style="font-family:Calibri,Arial,Helvetica,sans-serif; font-size:13.3333330154419px; background-color:rgb(255,255,255)">Microbiology
and Infecti</span><span style="font-family:Calibri,Arial,Helvetica,sans-serif; font-size:13.3333330154419px; background-color:rgb(255,255,255)">on Un</span><span style="font-family:Calibri,Arial,Helvetica,sans-serif; font-size:13.3333330154419px; background-color:rgb(255,255,255)">it)</span></span></div>
<div><span style="font-size:10pt">and the <a href="http://www2.warwick.ac.uk/fac/sci/chemistry/research/gibson/gibsongroup/" id="LPNoLP">Gibson Lab</a> (Warwick Chemistry)<br style="">
</span></div>
<div><span style="font-size:10pt"><br style="">
</span></div>
<div><span style="font-size:10pt">Twitter: <a href="https://twitter.com/JRJHealey" id="LPNoLP">
@JRJHealey</a> | </span><span style="font-size:10pt">Website: </span><a href="http://www2.warwick.ac.uk/fac/sci/moac/people/students/2013/joseph_healey" style="font-size:10pt" id="LPNoLP">MOAC Page</a> | ORCID: <span id="ms-rterangepaste-start"></span><span>orcid.org/0000-0002-9569-6738</span><span id="ms-rterangepaste-end"></span></div>
</div>
</div>
</div>
</div>
<hr style="display:inline-block;width:98%" tabindex="-1">
<div id="divRplyFwdMsg" dir="ltr"><font face="Calibri, sans-serif" style="font-size:11pt" color="#000000"><b>From:</b> Elaine Meng <meng@cgl.ucsf.edu><br>
<b>Sent:</b> 10 July 2018 18:00:39<br>
<b>To:</b> Healey, Joe<br>
<b>Cc:</b> chimera-users@cgl.ucsf.edu<br>
<b>Subject:</b> Re: [Chimera-users] Output chain sequences</font>
<div> </div>
</div>
<div class="BodyFragment"><font size="2"><span style="font-size:11pt;">
<div class="PlainText">Hi Joe,<br>
I can’t advise on the python, but our system was down for several days recently. It’s up now, and I just used the Align Chains service successfully.<br>
<br>
Saving fasta for structure chains might be slightly easier in ChimeraX, although still one-by-one. When you open a structure, there are links in the Log to show each chain sequence with a single click, and then you can save fasta using the context menu within
each sequence window.<br>
<<a href="http://rbvi.ucsf.edu/chimerax/docs/user/tools/sequenceviewer.html">http://rbvi.ucsf.edu/chimerax/docs/user/tools/sequenceviewer.html</a>><br>
<br>
Best,<br>
Elaine<br>
-----<br>
Elaine C. Meng, Ph.D. <br>
UCSF Chimera(X) team<br>
Department of Pharmaceutical Chemistry<br>
University of California, San Francisco<br>
<br>
<br>
> On Jul 10, 2018, at 4:48 AM, Healey, Joe <J.R.J.Healey@warwick.ac.uk> wrote:<br>
> <br>
> Hi Chimera Team,<br>
> <br>
> I've been experiencing issues with the "Align Chains" tools that connect to Clustal and Muscle - I think ostensibly this might be because the servers are no longer available or something.<br>
> <br>
> I'm happy to make the alignments myself, but to do this I'd like to try and simply export the sequences of all open models to a fasta file or similar. I know this can be done manually sequence-by-sequence thtrough the GUI.<br>
> <br>
> Could you tell me what the python (or chimera syntax) would be to do this if it's possible?<br>
> <br>
> I'm envisaging something to the effect of this, but I can't quite get what I need back in terms of the sequence (it returns a `bound object'?):<br>
> <br>
> ```<br>
> from chimera import openModels<br>
> all_mods = chimera.openModels.list(modelTypes=[chimera.Molecule])<br>
> with open('output.fasta', 'w') as ofh:<br>
> for mod in all_mods:<br>
> ofh.write('>%s\n%s' % (mod.name, mod.sequence)<br>
> ```<br>
<br>
</div>
</span></font></div>
</body>
</html>