[cctbxbb] Problems with cctbx - Explore symmetry

Wed Feb 17 14:36:07 PST 2016

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 [cctbxbb-bounces at phenix-online.org] on behalf of Paul Adams [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 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” 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
> 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

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 ][ 1-510-495-2506 ]
--

_______________________________________________
cctbxbb mailing list
cctbxbb at phenix-online.org
http://phenix-online.org/mailman/listinfo/cctbxbb

-- 
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.
Any opinions expressed within this e-mail are those of the individual and not necessarily of Diamond Light Source Ltd. 
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.
Diamond Light Source Limited (company no. 4375679). Registered in England and Wales with its registered office at Diamond House, Harwell Science and Innovation Campus, Didcot, Oxfordshire, OX11 0DE, United Kingdom