<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">Thanks for getting back to me, I didn't realise it was as simple as that, though it turns out I may have been barking up the wrong tree somewhat.</p>
<p style="margin-top:0;margin-bottom:0"><br>
</p>
<p style="margin-top:0;margin-bottom:0">I assumed more of the structures I was using had symmetry information than it appears they do, as they are EM resolved generally (and are C6 symmetrical).</p>
<p style="margin-top:0;margin-bottom:0"><br>
</p>
<p style="margin-top:0;margin-bottom:0">I would expect I could achieve what I want with C6 symmetry, but as you can see in the images I've attached, the C6 symmetry is 'inside out', relative to the reference structure I'm trying to replicate. It looks like
I need to specify a different axis of symmetry, but to also tell it to 'flip' how the molecules are being placed.</p>
<p style="margin-top:0;margin-bottom:0"><br>
</p>
<p style="margin-top:0;margin-bottom:0">Here is my model in blue fitted well to a subunit of this structure (PDBID 1Y12)</p>
<p style="margin-top:0;margin-bottom:0"><img size="144488" contenttype="image/png" id="img624536" style="max-width: 99.9%; user-select: none;" tabindex="0" src="cid:c873ee63-b463-4526-b205-d767b2d8a803"><br>
I'm trying to replicate this donut shape, but it seems the model has no symmetry information I can use (sym #1 group #0 won't work , if #0 is the reference structure).</p>
<p style="margin-top:0;margin-bottom:0"><br>
</p>
<p style="margin-top:0;margin-bottom:0">This is what I get from sym #1 group C6, hopefully you can understand what I'm getting at.</p>
<p style="margin-top:0;margin-bottom:0"><br>
</p>
<p style="margin-top:0;margin-bottom:0"><img size="120922" contenttype="image/png" id="img125153" style="max-width: 99.9%; user-select: none;" tabindex="0" src="cid:3a1bfeea-8b2c-40b2-92cb-ff7e3ee0761a"><br>
I've attached the model I'm trying to position if you have any thoughts about how to achieve this.</p>
<p style="margin-top:0;margin-bottom:0"><br>
</p>
<p style="margin-top:0;margin-bottom:0">Hopefully there's a programmatic solution as I'll be intending to do this a number of times.</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">Many thanks - I hope I've explained myself clear enough!</p>
<p style="margin-top:0;margin-bottom:0"><br>
</p>
<p style="margin-top:0;margin-bottom:0">Joe</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> 18 April 2018 18:15:36<br>
<b>To:</b> Healey, Joe<br>
<b>Cc:</b> chimera-users@cgl.ucsf.edu<br>
<b>Subject:</b> Re: [Chimera-users] BIOMT symmetry matrices</font>
<div> </div>
</div>
<div class="BodyFragment"><font size="2"><span style="font-size:11pt;">
<div class="PlainText">Hi Joe,<br>
Besides the “group biomt” option of “sym,” there is also “group #N” where N is the model number of another model.
<br>
<<a href="http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/sym.html#options">http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/sym.html#options</a>><br>
<br>
However, I believe you would need to match your structure onto model N pretty well before using that.<br>
I hope this helps,<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>
> On Apr 18, 2018, at 9:43 AM, Healey, Joe <J.R.J.Healey@warwick.ac.uk> wrote:<br>
> <br>
> Hi Chimera Team,<br>
> <br>
> I'm familiar with the sym command within chimera, specifying particular degrees of rotational symmetry for instance.<br>
> <br>
> As the biological unit feature tends to work quite nicely for this for a number of the proteins that I'm working on, I was wondering if there is a simple way to apply the BIOMT matrix for one protein to another?<br>
> <br>
> The proteins I want to apply them to are homology models of the equivalent proteins, so their biological unit information should be meaningful.<br>
> <br>
> If its possible to do this in chimera that would be great, but if you have any alternative suggestions (perhaps its possible to copy the BIOMT lines from one PDB text file to another?<br>
> <br>
> Joe Healey<br>
> <br>
<br>
</div>
</span></font></div>
</body>
</html>