[cctbxbb] Problems with cctbx - Explore symmetry

Wed Feb 17 22:50:37 PST 2016

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]
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

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, ENIGMA Science Focus Area

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