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, [email protected] 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:[email protected]] 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, 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"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: [email protected] [[email protected]] on behalf of Paul Adams [[email protected]] 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, [email protected] 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: [email protected] 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 [ [email protected] ][ 1-510-495-2506 ] --

_______________________________________________ cctbxbb mailing list [email protected] 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

-- 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 [ [email protected] ][ 1-510-495-2506 ] --