[Cod-bugs] Possible COD errors

[Robert McMeeking - UKRI STFC]

Hi Saulius

Meaningful logs are a bit of a problem!  I encountered the problems when processing the CIF files to generate atom centred coordinate environment search data for use in our CrystalWorks system. The various examples crashed the processing software I have been using. I needed to do a bit of improvised detective work to home in on the specific CIFs and find out what caused the programs to crash.

The plan is to process new/modified CIFs each night. So tracking new errors as  they arrive should (hopefully) be manageable.  

In the meantime I append a couple of extra entries I omitted from the previous set. 

Also would a list be useful  of those entries which are without coordinates and which I believe are not flagged in the MySQL file?

Best Regards

Bob
================================================================================================

9013798
N2 ********** 0.45190 1.03750 0.96000 0.04830
Pb2 ********** 0.45190 1.03750 0.02000 0.04830
.
.
H21 ********** 0.45040 1.14880 1.00000 0.13000


9014271
H(51) 0.83800 0.08900 ********** 1.00000 0.04700

================================================================================================



-----Original Message-----
From: Saulius Gražulis [mailto:grazulis at ibt.lt] 
Sent: 12 April 2018 12:31
To: McMeeking, Robert (STFC,DL,SC)
Cc: cod-bugs at lists.crystallography.net
Subject: Re: Possible COD errors

Dear Robert,

On 2018-04-12 13:26, Robert McMeeking - UKRI STFC wrote:
> I have been doing some investigation into problems encountered when 
> processing COD CIF for the CrystalWorks system at Daresbury.
> 
> Some entries have some incorrect coordinates - most cases it is 
> possible that decimal points have been lost. In one cases cell 
> dimensions are missing. In other cases my symmetry operator parsing 
> fails because more there is more than one symmetry operator per line 
> line with the "_loop" format. I am not fully clear what the standard 
> is for that!
> 
> Also there no coordinates present, but there is no "no coordinates"
> flag  in the MySQL database. I can send examples if that would be 
> helpful.
> 
> I append some error examples.

Thank you very much for your bug report, we'll have how this can be fixed.

If you have an exhaustive error list in machine-readable form (something like processing logs from your programs), this could be very helpful.

Cheers,
Saulius

--
Dr. Saulius Gražulis
Vilnius University Institute of Biotechnology, Saulėtekio al. 7
LT-10257 Vilnius, Lietuva (Lithuania)
fax: (+370-5)-2234367 / phone (office): (+370-5)-2234353
mobile: (+370-684)-49802, (+370-614)-36366