[cctbxbb] Problems with cctbx - Explore symmetry

Fri Feb 19 01:01:53 PST 2016

Thanks Nick

The bug now seems to be fixed and the calcite structure displays correctly via the link:

http://cds.dl.ac.uk/cgi-bin/rfm/crystalworks_365?Feb17

Bob

From: Nicholas Sauter [mailto:nksauter at lbl.gov]
Sent: 18 February 2016 20:01
To: McMeeking, Robert (STFC,DL,SC)
Cc: Paul Adams; Gildea, Richard (DLSLtd,RAL,LSCI); cctbx mailing list; phenixdev
Subject: Re: [cctbxbb] Problems with cctbx - Explore symmetry

OK, I've made a tiny change that will both safeguard our web security and permit the quotation marks to be interpreted correctly.

We'll need to follow whatever feedback the LBNL security team sends us, after they scan our site again.

Nick

Nicholas K. Sauter, Ph. D.
Computer Staff Scientist, Molecular Biophysics and Integrated Bioimaging Division
Lawrence Berkeley National Laboratory
1 Cyclotron Rd., Bldg. 33R0345
Berkeley, CA 94720
(510) 486-5713

On Wed, Feb 17, 2016 at 11:19 PM, <robert.mcmeeking at stfc.ac.uk<mailto:robert.mcmeeking at stfc.ac.uk>> wrote:
Is there a further possible complication with non-ascii (?) angled open and close quote symbols?

Bob

-----Original Message-----
From: Paul Adams [mailto:pdadams at lbl.gov<mailto:pdadams at lbl.gov>]
Sent: 18 February 2016 07:09
To: McMeeking, Robert (STFC,DL,SC)
Cc: Nicholas Sauter; Gildea, Richard (DLSLtd,RAL,LSCI); cctbxbb at phenix-online.org<mailto:cctbxbb at phenix-online.org>; developers at phenix-online.org<mailto:developers at phenix-online.org>
Subject: Re: [cctbxbb] Problems with cctbx - Explore symmetry

I think that the non-alpha numerics are: - * ‘ “

Some might not be used for the standard settings, but they should be allowed.

> On Feb 17, 2016, at 10:50 PM, robert.mcmeeking at stfc.ac.uk<mailto:robert.mcmeeking at stfc.ac.uk> wrote:
>
> Nick
>
> The link: http://cci.lbl.gov/sginfo/hall_symbols.html
>
> 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.
>
> Regards
>
> Bob McM
>
>
>
>
> From: Nicholas Sauter [mailto:nksauter at lbl.gov<mailto:nksauter at lbl.gov>]
> Sent: 17 February 2016 23:23
> To: Gildea, Richard (DLSLtd,RAL,LSCI)
> Cc: cctbx mailing list; McMeeking, Robert (STFC,DL,SC); phenixdev
> Subject: Re: [cctbxbb] Problems with cctbx - Explore symmetry
>
> Richard,
>
> 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?
>
> Nick
>
> Nicholas K. Sauter, Ph. D.
> Computer Staff Scientist, Molecular Biophysics and Integrated
> Bioimaging Division Lawrence Berkeley National Laboratory
> 1 Cyclotron Rd., Bldg. 33R0345
> Berkeley, CA 94720
> (510) 486-5713<tel:%28510%29%20486-5713>
>
> On Wed, Feb 17, 2016 at 2:36 PM, <richard.gildea at diamond.ac.uk<mailto:richard.gildea at diamond.ac.uk>> wrote:
> Hi Paul,
>
> I think this recent commit from Nick (23rd Jan 2016) is the culprit:
>
> https://sourceforge.net/p/cctbx/code/23627/
>
> This code snippet demonstrates the issue:
>
> $ cctbx.python
> Python 2.7.10 (default, Aug 28 2015, 12:10:46) [GCC 4.8.2 20140120
> (Red Hat 4.8.2-15)] on linux2 Type "help", "copyright", "credits" or
> "license" for more information.
> >>> sgsymbol = '-R 3 2"c'
> >>> lines_old = sgsymbol.replace("\015", "\012").split("\012") print
> >>> lines_old
> ['-R 3 2"c']
> >>> import cgi
> >>> lines_new = cgi.escape(sgsymbol,True).replace("\015",
> >>> "\012").split("\012") print lines_new
> ['-R 3 2&quot;c']
>
> Cheers,
>
> Richard
>
> Dr Richard Gildea
> Data Analysis Scientist
> Tel: +441235 77 8078
>
> Diamond Light Source Ltd.
> Diamond House
> Harwell Science & Innovation Campus
> Didcot
> Oxfordshire
> OX11 0DE
>
> ________________________________________
> From: cctbxbb-bounces at phenix-online.org<mailto:cctbxbb-bounces at phenix-online.org>
> [cctbxbb-bounces at phenix-online.org<mailto:cctbxbb-bounces at phenix-online.org>] on behalf of Paul Adams
> [pdadams at lbl.gov<mailto:pdadams at lbl.gov>]
> Sent: 17 February 2016 21:50
> To: McMeeking, Robert (STFC,DL,SC)
> Cc: phenixdev; cctbx mailing list
> Subject: Re: [cctbxbb] Problems with cctbx - Explore symmetry
>
> Hi Bob,
>
>   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.
>
>   Cheers,
>         Paul
>
> > On Feb 17, 2016, at 4:24 AM, robert.mcmeeking at stfc.ac.uk<mailto:robert.mcmeeking at stfc.ac.uk> wrote:
> >
> > Dear Colleagues
> >
> > I may not have sent my previous message to the most appropriate email address. I now forward including the “phenix-online.org<http://phenix-online.org>” one. Is there anyone out there who can point me in the right direction?
> >
> > Best Regards
> >
> > Bob
> >
> > From: McMeeking, Robert (STFC,DL,SC)
> > Sent: 13 February 2016 12:18
> > To: cctbx at cci.lbl.gov<mailto:cctbx at cci.lbl.gov>
> > Cc: McMeeking, Robert (STFC,DL,SC)
> > Subject: Problems with cctbx - Explore symmetry
> >
> > Hello from the UK
> >
> > I am currently experiencing problems with the Explore symmetry web service - http://cci.lbl.gov/cctbx/explore_symmetry.html. When dealing with a particular Hall Symbol there is a cctbx runtime error (Malformed matrix symbol).
> >
> > The symbol in question is:  -R 3 2"c It represents a setting for
> > Space Group R -3 c :H (167)
> >
> > 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.
> >
> > By way of background:
> >
> > 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.
> >
> > Inoticed the problem when using our CrystalWorks system to attempt
> > to display entries from the Crystallography365 Project
> >
> > http://cds.dl.ac.uk/cgi-bin/rfm/crystalworks_365?Feb17
> >
> > Best Regards
> >
> > Bob
> >
> > Dr R.F. McMeeking
> > Honorary Scientist
> > STFC Chemical Database Service at Daresbury
>
> --
> Paul Adams
> 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,
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> Building 80, Room 247
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>
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> Berkeley, CA 94720, USA.
>
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--
Paul Adams
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

Building 33, Room 347
Building 80, Room 247
Building 978, Room 4126
Tel: 1-510-486-4225, Fax: 1-510-486-5909 http://cci.lbl.gov/paul

Lawrence Berkeley Laboratory
1 Cyclotron Road
BLDG 33R0345
Berkeley, CA 94720, USA.

Executive Assistant: Louise Benvenue [ LBenvenue at lbl.gov<mailto:LBenvenue at lbl.gov> ][ 1-510-495-2506<tel:%5B%201-510-495-2506> ]
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