<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=utf-8">
<meta name="Generator" content="Microsoft Word 14 (filtered medium)">
<style><!--
/* Font Definitions */
@font-face
{font-family:Calibri;
panose-1:2 15 5 2 2 2 4 3 2 4;}
@font-face
{font-family:Tahoma;
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:12.0pt;
font-family:"Times New Roman","serif";}
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.MsoAcetate, li.MsoAcetate, div.MsoAcetate
{mso-style-priority:99;
mso-style-link:"Balloon Text Char";
margin:0cm;
margin-bottom:.0001pt;
font-size:8.0pt;
font-family:"Tahoma","sans-serif";}
span.im
{mso-style-name:im;}
span.BalloonTextChar
{mso-style-name:"Balloon Text Char";
mso-style-priority:99;
mso-style-link:"Balloon Text";
font-family:"Tahoma","sans-serif";
mso-fareast-language:EN-GB;}
span.EmailStyle20
{mso-style-type:personal-reply;
font-family:"Calibri","sans-serif";
color:#1F497D;}
.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;}
--></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"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D">Thanks Nick<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D"><o:p> </o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D">The bug now seems to be fixed and the calcite structure displays correctly via the link:<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D"><o:p> </o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D"><a href="http://cds.dl.ac.uk/cgi-bin/rfm/crystalworks_365?Feb17">http://cds.dl.ac.uk/cgi-bin/rfm/crystalworks_365?Feb17</a><o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D"><o:p> </o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D">Bob<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D"><o:p> </o:p></span></p>
<p class="MsoNormal"><b><span lang="EN-US" style="font-size:10.0pt;font-family:"Tahoma","sans-serif"">From:</span></b><span lang="EN-US" style="font-size:10.0pt;font-family:"Tahoma","sans-serif""> Nicholas Sauter [mailto:nksauter@lbl.gov]
<br>
<b>Sent:</b> 18 February 2016 20:01<br>
<b>To:</b> McMeeking, Robert (STFC,DL,SC)<br>
<b>Cc:</b> Paul Adams; Gildea, Richard (DLSLtd,RAL,LSCI); cctbx mailing list; phenixdev<br>
<b>Subject:</b> Re: [cctbxbb] Problems with cctbx - Explore symmetry<o:p></o:p></span></p>
<p class="MsoNormal"><o:p> </o:p></p>
<div>
<p class="MsoNormal">OK, I've made a tiny change that will both safeguard our web security and permit the quotation marks to be interpreted correctly. <o:p></o:p></p>
<div>
<p class="MsoNormal"><o:p> </o:p></p>
</div>
<div>
<p class="MsoNormal">We'll need to follow whatever feedback the LBNL security team sends us, after they scan our site again. <o:p></o:p></p>
</div>
<div>
<p class="MsoNormal"><o:p> </o:p></p>
</div>
<div>
<p class="MsoNormal">Nick<o:p></o:p></p>
</div>
</div>
<div>
<p class="MsoNormal"><br clear="all">
<o:p></o:p></p>
<div>
<div>
<div>
<div>
<p class="MsoNormal">Nicholas K. Sauter, Ph. D.<br>
Computer Staff Scientist, Molecular Biophysics and Integrated Bioimaging Division<o:p></o:p></p>
<div>
<p class="MsoNormal">Lawrence Berkeley National Laboratory<br>
1 Cyclotron Rd., Bldg. 33R0345<br>
Berkeley, CA 94720<br>
(510) 486-5713<o:p></o:p></p>
</div>
</div>
</div>
</div>
</div>
<p class="MsoNormal"><o:p> </o:p></p>
<div>
<p class="MsoNormal">On Wed, Feb 17, 2016 at 11:19 PM, <<a href="mailto:robert.mcmeeking@stfc.ac.uk" target="_blank">robert.mcmeeking@stfc.ac.uk</a>> wrote:<o:p></o:p></p>
<p class="MsoNormal">Is there a further possible complication with non-ascii (?) angled open and close quote symbols?<br>
<br>
Bob<br>
<br>
<br>
<span class="im">-----Original Message-----</span><br>
<span class="im">From: Paul Adams [mailto:<a href="mailto:pdadams@lbl.gov">pdadams@lbl.gov</a>]</span><br>
<span class="im">Sent: 18 February 2016 07:09</span><br>
<span class="im">To: McMeeking, Robert (STFC,DL,SC)</span><o:p></o:p></p>
<div>
<div>
<p class="MsoNormal" style="margin-bottom:12.0pt">Cc: Nicholas Sauter; Gildea, Richard (DLSLtd,RAL,LSCI);
<a href="mailto:cctbxbb@phenix-online.org">cctbxbb@phenix-online.org</a>; <a href="mailto:developers@phenix-online.org">
developers@phenix-online.org</a><br>
Subject: Re: [cctbxbb] Problems with cctbx - Explore symmetry<br>
<br>
<br>
I think that the non-alpha numerics are: - * ‘ “<br>
<br>
Some might not be used for the standard settings, but they should be allowed.<br>
<br>
> On Feb 17, 2016, at 10:50 PM, <a href="mailto:robert.mcmeeking@stfc.ac.uk">robert.mcmeeking@stfc.ac.uk</a> wrote:<br>
><br>
> Nick<br>
><br>
> The link: <a href="http://cci.lbl.gov/sginfo/hall_symbols.html" target="_blank">
http://cci.lbl.gov/sginfo/hall_symbols.html</a><br>
><br>
> gives a list of some possible Hall symbols. Other valid symbols are, I presume, possible. But on a quick glance, the single quote does not seem to feature – others may know more about what symbols are valid.<br>
><br>
> Regards<br>
><br>
> Bob McM<br>
><br>
><br>
><br>
><br>
> From: Nicholas Sauter [mailto:<a href="mailto:nksauter@lbl.gov">nksauter@lbl.gov</a>]<br>
> Sent: 17 February 2016 23:23<br>
> To: Gildea, Richard (DLSLtd,RAL,LSCI)<br>
> Cc: cctbx mailing list; McMeeking, Robert (STFC,DL,SC); phenixdev<br>
> Subject: Re: [cctbxbb] Problems with cctbx - Explore symmetry<br>
><br>
> Richard,<br>
><br>
> We filtered double quotes (") out of the web input for computer-security purposes. Could you perhaps let me know what special characters we need to allow? Specifically do I need to allow both single (') and double quotes, or just double?<br>
><br>
> Nick<br>
><br>
> Nicholas K. Sauter, Ph. D.<br>
> Computer Staff Scientist, Molecular Biophysics and Integrated<br>
> Bioimaging Division Lawrence Berkeley National Laboratory<br>
> 1 Cyclotron Rd., Bldg. 33R0345<br>
> Berkeley, CA 94720<br>
> <a href="tel:%28510%29%20486-5713">(510) 486-5713</a><br>
><br>
> On Wed, Feb 17, 2016 at 2:36 PM, <<a href="mailto:richard.gildea@diamond.ac.uk">richard.gildea@diamond.ac.uk</a>> wrote:<br>
> Hi Paul,<br>
><br>
> I think this recent commit from Nick (23rd Jan 2016) is the culprit:<br>
><br>
> <a href="https://sourceforge.net/p/cctbx/code/23627/" target="_blank">https://sourceforge.net/p/cctbx/code/23627/</a><br>
><br>
> This code snippet demonstrates the issue:<br>
><br>
> $ cctbx.python<br>
> Python 2.7.10 (default, Aug 28 2015, 12:10:46) [GCC 4.8.2 20140120<br>
> (Red Hat 4.8.2-15)] on linux2 Type "help", "copyright", "credits" or<br>
> "license" for more information.<br>
> >>> sgsymbol = '-R 3 2"c'<br>
> >>> lines_old = sgsymbol.replace("\015", "\012").split("\012") print<br>
> >>> lines_old<br>
> ['-R 3 2"c']<br>
> >>> import cgi<br>
> >>> lines_new = cgi.escape(sgsymbol,True).replace("\015",<br>
> >>> "\012").split("\012") print lines_new<br>
> ['-R 3 2&quot;c']<br>
><br>
> Cheers,<br>
><br>
> Richard<br>
><br>
> Dr Richard Gildea<br>
> Data Analysis Scientist<br>
> Tel: +441235 77 8078<br>
><br>
> Diamond Light Source Ltd.<br>
> Diamond House<br>
> Harwell Science & Innovation Campus<br>
> Didcot<br>
> Oxfordshire<br>
> OX11 0DE<br>
><br>
> ________________________________________<br>
> From: <a href="mailto:cctbxbb-bounces@phenix-online.org">cctbxbb-bounces@phenix-online.org</a><br>
> [<a href="mailto:cctbxbb-bounces@phenix-online.org">cctbxbb-bounces@phenix-online.org</a>] on behalf of Paul Adams<br>
> [<a href="mailto:pdadams@lbl.gov">pdadams@lbl.gov</a>]<br>
> Sent: 17 February 2016 21:50<br>
> To: McMeeking, Robert (STFC,DL,SC)<br>
> Cc: phenixdev; cctbx mailing list<br>
> Subject: Re: [cctbxbb] Problems with cctbx - Explore symmetry<br>
><br>
> Hi Bob,<br>
><br>
> thanks for the email. I can reproduce this problem. Is anyone aware of any changes that have been made in the space group handling in the last year or two? This is code that doesn’t change much, if at all.<br>
><br>
> Cheers,<br>
> Paul<br>
><br>
> > On Feb 17, 2016, at 4:24 AM, <a href="mailto:robert.mcmeeking@stfc.ac.uk">robert.mcmeeking@stfc.ac.uk</a> wrote:<br>
> ><br>
> > Dear Colleagues<br>
> ><br>
> > I may not have sent my previous message to the most appropriate email address. I now forward including the “<a href="http://phenix-online.org" target="_blank">phenix-online.org</a>” one. Is there anyone out there who can point me in the right direction?<br>
> ><br>
> > Best Regards<br>
> ><br>
> > Bob<br>
> ><br>
> > From: McMeeking, Robert (STFC,DL,SC)<br>
> > Sent: 13 February 2016 12:18<br>
> > To: <a href="mailto:cctbx@cci.lbl.gov">cctbx@cci.lbl.gov</a><br>
> > Cc: McMeeking, Robert (STFC,DL,SC)<br>
> > Subject: Problems with cctbx - Explore symmetry<br>
> ><br>
> > Hello from the UK<br>
> ><br>
> > I am currently experiencing problems with the Explore symmetry web service - <a href="http://cci.lbl.gov/cctbx/explore_symmetry.html" target="_blank">
http://cci.lbl.gov/cctbx/explore_symmetry.html</a>. When dealing with a particular Hall Symbol there is a cctbx runtime error (Malformed matrix symbol).<br>
> ><br>
> > The symbol in question is: -R 3 2"c It represents a setting for<br>
> > Space Group R -3 c :H (167)<br>
> ><br>
> > I am practically certain this worked fine in the past. I suspect the problem may be related to parsing the double quote symbol. If I replace with a single quote it manages to run OK, but the output information is a non-standard setting for Space Group 165.<br>
> ><br>
> > By way of background:<br>
> ><br>
> > I call the web service from my own CGI script and extract the symmetry operators that I need to display the crystal structure in question. The Hall symbol used is from the Crystallographic Open Database CIF (COD 2100992). I noticed the problem very recently,
but because I cache information it is not clear when the problem first appeared. I only need to go through this process when explicit symmetry operators are not present in the CIF in question. I have not, as yet, installed the cctbx system on our server.<br>
> ><br>
> > Inoticed the problem when using our CrystalWorks system to attempt<br>
> > to display entries from the Crystallography365 Project<br>
> ><br>
> > <a href="http://cds.dl.ac.uk/cgi-bin/rfm/crystalworks_365?Feb17" target="_blank">
http://cds.dl.ac.uk/cgi-bin/rfm/crystalworks_365?Feb17</a><br>
> ><br>
> > Best Regards<br>
> ><br>
> > Bob<br>
> ><br>
> > Dr R.F. McMeeking<br>
> > Honorary Scientist<br>
> > STFC Chemical Database Service at Daresbury<br>
><br>
> --<br>
> Paul Adams<br>
> Interim Division Director, Molecular Biophysics & Integrated<br>
> Bioimaging, Lawrence Berkeley Lab Division Deputy for Biosciences,<br>
> Advanced Light Source, Lawrence Berkeley Lab Adjunct Professor,<br>
> Department of Bioengineering, U.C. Berkeley Vice President for<br>
> Technology, the Joint BioEnergy Institute Laboratory Research Manager,<br>
> ENIGMA Science Focus Area<br>
><br>
> Building 33, Room 347<br>
> Building 80, Room 247<br>
> Building 978, Room 4126<br>
> Tel: <a href="tel:1-510-486-4225">1-510-486-4225</a>, Fax: <a href="tel:1-510-486-5909">
1-510-486-5909</a> <a href="http://cci.lbl.gov/paul" target="_blank">http://cci.lbl.gov/paul</a><br>
><br>
> Lawrence Berkeley Laboratory<br>
> 1 Cyclotron Road<br>
> BLDG 33R0345<br>
> Berkeley, CA 94720, USA.<br>
><br>
> Executive Assistant: Louise Benvenue [ <a href="mailto:LBenvenue@lbl.gov">LBenvenue@lbl.gov</a> ][<br>
> <a href="tel:1-510-495-2506">1-510-495-2506</a> ]<br>
> --<br>
><br>
><br>
><br>
><br>
><br>
><br>
><br>
><br>
><br>
><br>
><br>
><br>
><br>
><br>
><br>
> _______________________________________________<br>
> cctbxbb mailing list<br>
> <a href="mailto:cctbxbb@phenix-online.org">cctbxbb@phenix-online.org</a><br>
> <a href="http://phenix-online.org/mailman/listinfo/cctbxbb" target="_blank">http://phenix-online.org/mailman/listinfo/cctbxbb</a><br>
><br>
> --<br>
> This e-mail and any attachments may contain confidential, copyright and or privileged material, and are for the use of the intended addressee only. If you are not the intended addressee or an authorised recipient of the addressee please notify us of receipt
by returning the e-mail and do not use, copy, retain, distribute or disclose the information in or attached to the e-mail.<br>
> Any opinions expressed within this e-mail are those of the individual and not necessarily of Diamond Light Source Ltd.<br>
> Diamond Light Source Ltd. cannot guarantee that this e-mail or any attachments are free from viruses and we cannot accept liability for any damage which you may sustain as a result of software viruses which may be transmitted in or with the message.<br>
> Diamond Light Source Limited (company no. 4375679). Registered in<br>
> England and Wales with its registered office at Diamond House, Harwell<br>
> Science and Innovation Campus, Didcot, Oxfordshire, OX11 0DE, United<br>
> Kingdom<br>
><br>
<br>
--<br>
Paul Adams<br>
Interim Division Director, Molecular Biophysics & Integrated Bioimaging, Lawrence Berkeley Lab Division Deputy for Biosciences, Advanced Light Source, Lawrence Berkeley Lab Adjunct Professor, Department of Bioengineering, U.C. Berkeley Vice President for Technology,
the Joint BioEnergy Institute Laboratory Research Manager, ENIGMA Science Focus Area<br>
<br>
Building 33, Room 347<br>
Building 80, Room 247<br>
Building 978, Room 4126<br>
Tel: 1-510-486-4225, Fax: 1-510-486-5909 <a href="http://cci.lbl.gov/paul" target="_blank">
http://cci.lbl.gov/paul</a><br>
<br>
Lawrence Berkeley Laboratory<br>
1 Cyclotron Road<br>
BLDG 33R0345<br>
Berkeley, CA 94720, USA.<br>
<br>
Executive Assistant: Louise Benvenue [ <a href="mailto:LBenvenue@lbl.gov">LBenvenue@lbl.gov</a> ]<a href="tel:%5B%201-510-495-2506">[ 1-510-495-2506</a> ]<br>
--<br>
<br>
<br>
<br>
<br>
<br>
<br>
<br>
<br>
<br>
<br>
<br>
<br>
<br>
<o:p></o:p></p>
</div>
</div>
</div>
<p class="MsoNormal"><o:p> </o:p></p>
</div>
</div>
</body>
</html>