[Cod-bugs] Fwd: Undercounting of structure factors

[Andrius Merkys]

Sveiki,

Persiunčiu Tomo atsakymą man dėl HKL failų.

Iki,
Andrius


-------- Forwarded Message --------
Subject: Re: [Cod-bugs] Undercounting of structure factors
Date: Thu, 8 Apr 2021 20:14:42 +0200
From: Thomas Munro <thomas.a.munro at gmail.com>
To: Andrius Merkys <andrius.merkys at gmail.com>

Hi Andrius,
no worries about the delay. Sorry to pester you again! I’m a great
admirer of the vast resource you’ve put together.
I’m not capable of writing the code myself, but I’ll see if I can find
something. I’d be happy to contribute to a bounty if it has to be
written. That might be worth exploring if the database is short on
funds.
Cheers,
Thomas

On 08/04/2021, Andrius Merkys <andrius.merkys at gmail.com> wrote:
> Hi Thomas,
>
> Thank you for your message and sorry about the delay to respond.
>
> We in the COD are aware about this undercounting. The way we would like
> to deal with it is to extract the HKL data embedded in CIF files and
> place it in separate HKL files, so that the representation of HKL in the
> COD be homogeneous.
>
> However, currently we lack workforce to implement this. If you would be
> willing to contribute a program for HKL data extraction, we could
> include it in the data processing pipeline. Our requirements for the
> program are free/libre open source software, usable unsupervised in
> Linux command line environment.
>
> Best wishes,
> Andrius Merkys (on behalf of the Crystallography Open Database)
>
> On 2021-03-23 18:30, Thomas Munro wrote:
>> Hi,
>> I’m a huge fan of your work. It’s tragic that the CCDC is still so
>> closed-minded.
>> I'm not a trained crystallographer, so I may have misunderstood this,
>> but I notice that only a small fraction of COD entries are returned
>> under the “has Fobs” filter. This seems to refer to having a separate
>> hkl file. But checking recent structures without one, I find that
>> about half of them have the hkl data embedded in the cif. So I thought
>> it might be useful for users to flag these as well, so that the filter
>> would return many more examples. Presumably it would be
>> straightforward to detect them with a regular expression, or even just
>> by their much larger file size, and update the indexing. Just a
>> thought! Keep up the good work.
>> Cheers,
>> Thomas
>
> --
> Dr. Andrius Merkys
> Vilnius University Institute of Biotechnology, Saulėtekio al. 7
> LT-10257 Vilnius, Lithuania
>

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