From chenghua at rcsb.rutgers.edu  Sat Apr 29 18:20:54 2023
From: chenghua at rcsb.rutgers.edu (Chenghua Shao)
Date: Sat, 29 Apr 2023 11:20:54 -0400
Subject: [Cod-bugs] Question on missing sdf file for COD entry
Message-ID: <bebb7443-a328-091c-093e-2ba9bed0643f@rcsb.rutgers.edu>

Hi,

Could you please let me know under what condition the sdf file for a COD 
entry is missing? e.g.
2204850 is a valid entry, but there is no sdf file at

https://molecules.crystallography.net/cod/sdf/2/20/48/2204850.sdf

Thanks!

-- 
=============================================
CHENGHUA SHAO, Ph.D.
Scientific Software Developer, RCSB Protein Data Bank
Assistant Research Professor, Institute for Quantitative Biomedicine
Rutgers, The State University of New Jersey
174 Frelinghuysen Road, Piscataway NJ 08854
P: 848.445.4968 | E: chenghua.shao at rcsb.org
rcsb.org <www.rcsb.org> | iqb.rutgers.edu | facebook 
<https://www.facebook.com/RCSBPDB> | twitter 
<https://twitter.com/buildmodels> | PDB-Carbohydrate 
<https://doi.org/10.1093/glycob/cwab039>
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From antanas.vaitkus90 at gmail.com  Sat Apr 29 18:51:05 2023
From: antanas.vaitkus90 at gmail.com (Antanas Vaitkus)
Date: Sat, 29 Apr 2023 18:51:05 +0300
Subject: [Cod-bugs] Question on missing sdf file for COD entry
In-Reply-To: <bebb7443-a328-091c-093e-2ba9bed0643f@rcsb.rutgers.edu>
References: <bebb7443-a328-091c-093e-2ba9bed0643f@rcsb.rutgers.edu>
Message-ID: <CALHYoX4q17CKcUOYLv=jDYVnazPwaOw+FC2wT=RcZ=DqqYG2qQ@mail.gmail.com>

Dear Chenghua Shao,

Entry 2204850 is not included in the SDF set since it was recognised as a
polymeric molecule (a molecule that spans an infinite number of unit
cells). Sadly, the CIF to SDF conversion software that we use is currently
not able to process such entries.

Hope this helps.

Sincerely,
Antanas Vaitkus

On Sat, 29 Apr 2023 at 18:46, Chenghua Shao <chenghua at rcsb.rutgers.edu>
wrote:

> Hi,
>
> Could you please let me know under what condition the sdf file for a COD
> entry is missing? e.g.
> 2204850 is a valid entry, but there is no sdf file at
>
> https://molecules.crystallography.net/cod/sdf/2/20/48/2204850.sdf
>
> Thanks!
> --
> =============================================
> CHENGHUA SHAO, Ph.D.
> Scientific Software Developer, RCSB Protein Data Bank
> Assistant Research Professor, Institute for Quantitative Biomedicine
> Rutgers, The State University of New Jersey
> 174 Frelinghuysen Road, Piscataway NJ 08854
> P: 848.445.4968 | E: chenghua.shao at rcsb.org
> rcsb.org <http://www.rcsb.org> | iqb.rutgers.edu | facebook
> <https://www.facebook.com/RCSBPDB> | twitter
> <https://twitter.com/buildmodels> | PDB-Carbohydrate
> <https://doi.org/10.1093/glycob/cwab039>
>
> --
> This message has been scanned for viruses and
> dangerous content by *MailScanner* <http://www.mailscanner.info/>, and is
> believed to be clean.
> _______________________________________________
> Cod-bugs mailing list
> Cod-bugs at lists.crystallography.net
> http://lists.crystallography.net/cgi-bin/mailman/listinfo/cod-bugs
>


-- 
Antanas Vaitkus,
Vilnius University,
Life Sciences Center,
Institute of Biotechnology,
room C521, Saul?tekio al. 7,
LT-10257 Vilnius, Lithuania

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From chenghua at rcsb.rutgers.edu  Sun Apr 30 23:50:16 2023
From: chenghua at rcsb.rutgers.edu (Chenghua Shao)
Date: Sun, 30 Apr 2023 16:50:16 -0400
Subject: [Cod-bugs] Question on missing sdf file for COD entry
In-Reply-To: <CALHYoX4q17CKcUOYLv=jDYVnazPwaOw+FC2wT=RcZ=DqqYG2qQ@mail.gmail.com>
References: <bebb7443-a328-091c-093e-2ba9bed0643f@rcsb.rutgers.edu>
 <CALHYoX4q17CKcUOYLv=jDYVnazPwaOw+FC2wT=RcZ=DqqYG2qQ@mail.gmail.com>
Message-ID: <5fdab3d1-41b1-2642-ed8e-4c9c072cc682@rcsb.rutgers.edu>

Thanks Antanas!

=============================================
CHENGHUA SHAO, Ph.D.
Scientific Software Developer, RCSB Protein Data Bank
Assistant Research Professor, Institute for Quantitative Biomedicine
Rutgers, The State University of New Jersey
174 Frelinghuysen Road, Piscataway NJ 08854
P: 848.445.4968 | E: chenghua.shao at rcsb.org
rcsb.org <www.rcsb.org> | iqb.rutgers.edu | facebook 
<https://www.facebook.com/RCSBPDB> | twitter 
<https://twitter.com/buildmodels> | PDB-Carbohydrate 
<https://doi.org/10.1093/glycob/cwab039>
On 4/29/23 11:51, Antanas Vaitkus wrote:
> Dear Chenghua Shao,
>
> Entry 2204850 is not included in the SDF set since it was recognised 
> as a polymeric molecule (a molecule that spans an infinite number of 
> unit cells). Sadly, the CIF to SDF conversion software that we use is 
> currently not able to process such entries.
>
> Hope this helps.
>
> Sincerely,
> Antanas Vaitkus
>
> On Sat, 29 Apr 2023 at 18:46, Chenghua Shao 
> <chenghua at rcsb.rutgers.edu> wrote:
>
>     Hi,
>
>     Could you please let me know under what condition the sdf file for
>     a COD entry is missing? e.g.
>     2204850 is a valid entry, but there is no sdf file at
>
>     https://molecules.crystallography.net/cod/sdf/2/20/48/2204850.sdf
>
>     Thanks!
>
>     -- 
>     =============================================
>     CHENGHUA SHAO, Ph.D.
>     Scientific Software Developer, RCSB Protein Data Bank
>     Assistant Research Professor, Institute for Quantitative Biomedicine
>     Rutgers, The State University of New Jersey
>     174 Frelinghuysen Road, Piscataway NJ 08854
>     P: 848.445.4968 | E: chenghua.shao at rcsb.org
>     rcsb.org <http://www.rcsb.org> | iqb.rutgers.edu
>     <http://iqb.rutgers.edu> | facebook
>     <https://www.facebook.com/RCSBPDB> | twitter
>     <https://twitter.com/buildmodels> | PDB-Carbohydrate
>     <https://doi.org/10.1093/glycob/cwab039>
>
>     -- 
>     This message has been scanned for viruses and
>     dangerous content by *MailScanner* <http://www.mailscanner.info/>,
>     and is
>     believed to be clean.
>     _______________________________________________
>     Cod-bugs mailing list
>     Cod-bugs at lists.crystallography.net
>     http://lists.crystallography.net/cgi-bin/mailman/listinfo/cod-bugs
>
>
>
> -- 
> Antanas Vaitkus,
> Vilnius University,
> Life Sciences Center,
> Institute of Biotechnology,
> room C521, Saul?tekio al. 7,
> LT-10257 Vilnius, Lithuania
>
>
-- 
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