From andrius.merkys at gmail.com  Mon Apr 12 11:07:46 2021
From: andrius.merkys at gmail.com (Andrius Merkys)
Date: Mon, 12 Apr 2021 11:07:46 +0300
Subject: [Cod-bugs] Fwd:  Undercounting of structure factors
In-Reply-To: <CAJLaq7rzoV5w2j80QUXPLn1W4ponUvRLn0_AwXJv8hVXwg3dVQ@mail.gmail.com>
References: <CAJLaq7rzoV5w2j80QUXPLn1W4ponUvRLn0_AwXJv8hVXwg3dVQ@mail.gmail.com>
Message-ID: <c00b4904-83fa-abf4-9b8d-af8e872c2b32@gmail.com>

Sveiki,

Persiun?iu Tomo atsakym? man d?l HKL fail?.

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, Saul?tekio al. 7
> LT-10257 Vilnius, Lithuania
>

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From andrius.merkys at gmail.com  Mon Apr 12 11:13:06 2021
From: andrius.merkys at gmail.com (Andrius Merkys)
Date: Mon, 12 Apr 2021 11:13:06 +0300
Subject: [Cod-bugs] Fwd: Fwd: Extracting hkl from cif
In-Reply-To: <CAJLaq7qt+eq4AO6t67ZDp0-nyjBrxDZWofkKVaF4+1Ae_+4vPg@mail.gmail.com>
References: <CAJLaq7qt+eq4AO6t67ZDp0-nyjBrxDZWofkKVaF4+1Ae_+4vPg@mail.gmail.com>
Message-ID: <d4faafe2-bce2-98e5-31c7-f8453461b8d1@gmail.com>

Sveiki,

Persiun?iu antr? Tomo lai?k?.

Iki,
Andrius


-------- Forwarded Message --------
Subject: Fwd: Extracting hkl from cif
Date: Thu, 8 Apr 2021 22:14:07 +0200
From: Thomas Munro <thomas.a.munro at gmail.com>
To: Andrius Merkys <andrius.merkys at gmail.com>
CC: Daniel Kratzert <dkratzert at gmx.de>

Hi Andrius,
Daniel Kratzert says some of his python code should be adaptable to
your needs, and has kindly offered to help if needed.
https://github.com/dkratzert/FinalCif/blob/master/tools/shred.py
I certainly won?t be any use, but as mentioned, if funding is short, I
would be happy to contribute to bounties for tasks like this. Thanks
again, Daniel!
Cheers,
Thomas

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From ndoebelin at gmx.ch  Wed Apr 14 11:05:27 2021
From: ndoebelin at gmx.ch (=?UTF-8?Q?Nicola_D=C3=B6belin?=)
Date: Wed, 14 Apr 2021 10:05:27 +0200
Subject: [Cod-bugs] Question about Panalytical COD-derived search-match
 database
Message-ID: <trinity-137f52ba-a743-4687-994b-fafbbffba9ba-1618387527784@3c-app-gmx-bap56>

Hello,

On the "What's new" page of the COD you report the release of a COD-derived search-match database by Panalytical in March 2021. I am interested in accessing this database from a different software, but I am unsure about the copyright situation. Would it be legal to officially recommend downloading this database for use with a software that is not related to Panalytical?

Kind regards,
Nicola D?belin

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From grazulis at ibt.lt  Wed Apr 14 11:17:56 2021
From: grazulis at ibt.lt (=?UTF-8?Q?Saulius_Gra=c5=beulis?=)
Date: Wed, 14 Apr 2021 11:17:56 +0300
Subject: [Cod-bugs] Question about Panalytical COD-derived search-match
 database
In-Reply-To: <trinity-137f52ba-a743-4687-994b-fafbbffba9ba-1618387527784@3c-app-gmx-bap56>
References: <trinity-137f52ba-a743-4687-994b-fafbbffba9ba-1618387527784@3c-app-gmx-bap56>
Message-ID: <19909724-d388-a755-9afc-b8e3fb3c7986@ibt.lt>

Dear Nicola,

thank you for your inquirey.

On 2021-04-14 11:05, Nicola D?belin wrote:
> On the "What's new" page of the COD you report the release of a COD-derived search-match database by Panalytical in March 2021. I am interested in accessing this database from a different software, but I am unsure about the copyright situation. Would it be legal to officially recommend downloading this database for use with a software that is not related to Panalytical?
>
The COD data is FAIR and Open Access, so as far as the data goes you are
perfectly fine to fetch COD files and yours them with any software you
may wish.

As far as PANalytical <https://www.malvernpanalytical.com> software and
databases concern, I can not answer definitely since this is their (c)
software. I have forwarded your request to people in PANalytical
<https://www.malvernpanalytical.com> and hopefully they will get back to
you.

Sincerely yours,
Saulius

-- 
Dr. Saulius Gra?ulis
Vilnius University, Life Science Center, Institute of Biotechnology
Saul?tekio al. 7, LT-10257 Vilnius, Lietuva (Lithuania)
phone (office): (+370-5)-2234353, mobile: (+370-684)-49802, (+370-614)-36366

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From andrius.merkys at gmail.com  Fri Apr 16 20:08:22 2021
From: andrius.merkys at gmail.com (Andrius Merkys)
Date: Fri, 16 Apr 2021 20:08:22 +0300
Subject: [Cod-bugs] Fwd: Extracting hkl from cif
In-Reply-To: <CAJLaq7qt+eq4AO6t67ZDp0-nyjBrxDZWofkKVaF4+1Ae_+4vPg@mail.gmail.com>
References: <CAJLaq7p8LHPDAuaquhrzBSXKcJTAEyN5wPCmYSvaRhwxx8CR5w@mail.gmail.com>
 <01267C34-05FB-4844-B779-E2EBA10CE985@gmx.de>
 <CAJLaq7qt+eq4AO6t67ZDp0-nyjBrxDZWofkKVaF4+1Ae_+4vPg@mail.gmail.com>
Message-ID: <112e5b47-c919-9a7d-b7bd-fe7b2fc8e990@gmail.com>

Hi Thomas,

Thanks a lot for pointing me to FinalCif! I find the code there useful
indeed. I will see what I can do about converting SHELX HKL files to CIF.

Best wishes,
Andrius

On 2021-04-08 23:14, Thomas Munro wrote:
> Hi Andrius,
> Daniel Kratzert says some of his python code should be adaptable to
> your needs, and has kindly offered to help if needed.
> https://github.com/dkratzert/FinalCif/blob/master/tools/shred.py
> I certainly won?t be any use, but as mentioned, if funding is short, I
> would be happy to contribute to bounties for tasks like this. Thanks
> again, Daniel!
> Cheers,
> Thomas

-- 
Dr. Andrius Merkys
Vilnius University Institute of Biotechnology, Saul?tekio al. 7
LT-10257 Vilnius, Lithuania

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From vigneshwaran.p.s21 at gmail.com  Sat Apr 17 09:10:43 2021
From: vigneshwaran.p.s21 at gmail.com (vigneshwaran P)
Date: Sat, 17 Apr 2021 02:10:43 -0400
Subject: [Cod-bugs] (no subject)
Message-ID: <CANdaPtoT-W_Q2QmL2B1Eid+htbhgTFBMFpmSrzLuspjonYyq0g@mail.gmail.com>

hi sir,madam
i found a sensible data/directory disclosure on your site.
please verify it .
I'm attaching proof with this mail.


thanks.

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