[cctbxbb] Problems with cctbx - Explore symmetry

Paul Adams pdadams at lbl.gov
Wed Feb 17 13:50:06 PST 2016


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

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