From do-not-reply at stackoverflow.email  Tue May  5 17:39:15 2020
From: do-not-reply at stackoverflow.email (Stack Overflow)
Date: Tue, 05 May 2020 14:39:15 +0000 (UTC)
Subject: [Cod-bugs] {Disarmed} Invitation from Marcin Wojdyr
Message-ID: <fhdi-iE4Qx-VPZOGyIwWTw@ismtpd0039p1iad1.sendgrid.net>

Hello
Marcin Wojdyr told us you're *just* the right kind of expert the Materials Modeling Stack Exchange Q&A site needs.
Marcin Wojdyr also said: Hi, a few days ago a Materials Modelling site started to run as a sister site of StackOverflow. (For the first 2 weeks it's not visible publicly, as it may be terminated if the number of participant is low). Someone just asked there "How can I create a .CIF file from x-ray diffraction data in a paper" for a structure absent in CCDC. I thought it'd be a good opportunity to provide instruction and write about COD - for someone who know more than me about it. This new <a href="https://materials.stackexchange.com">Stack Exchange Q&A site</a> is currently in private beta, but since you've been recommended by a peer, we're giving you super secret access to get in early and help shape the community.
[GRANT ME ACCESS](https://materials.stackexchange.com/grant-beta-access?key=477168b9a20605271bf8f698b9e97d05a53b43fa588560bbce7d979e9e7603ac)


Stack Overflow, 110 William Street, 28th floor, New York, NY 10038 <3
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From nbehrnd at yahoo.com  Thu May  7 22:20:47 2020
From: nbehrnd at yahoo.com (Norwid Behrnd)
Date: Thu, 7 May 2020 21:20:47 +0200
Subject: [Cod-bugs] update suggest cod-tools, bash script molcif2sdf
References: <20200507212047.4170382e.ref@Carnot>
Message-ID: <20200507212047.4170382e@Carnot>

Dear Ladies and Gentlemen,

based on an observation I would like to suggest an update of bash
script molcif2sdf (last public edit by 2019-12-06) at line #114; namely,
the substitution of ?babel? by ?obabel?


During a session of Linux Debian 10, backed by openbabel (release
3.0.0), I aimed for the conversion of file 1501905.cif into a .sdf
suitable for DataWarrior with cod-tools' codcif2sdf.  The conversion
failed and indicated bash script molcif2sdf as possible cause:

norwid at carnot2:~/Desktop$ codcif2sdf 1501905.cif 
/usr/bin/cif_molecule: 1501905.cif data_1501905: WARNING, multiplicity
ratios are given instead of multiplicities for 61 atoms -- taking
calculated values.
/usr/bin/molcif2sdf: 114: babel: not found
norwid at carnot2:~/Desktop$ codcif2sdf --version
cod-tools version 2.10


A fresh re-installation from Debian's testing repositories did not
improve the situation, by label they are the same as the tools offered
by your page as tar.gz.  Tentatively, I substituted ?babel? by ?obabel?
in line #114 of molcif2sdf and found obtained the .sdf as expected.

norwid at carnot2:~/Desktop$ codcif2sdf 1501905.cif > so.sdf
/usr/bin/cif_molecule: 1501905.cif data_1501905: WARNING, multiplicity
ratios are given instead of multiplicities for 61 atoms -- taking
calculated values. 1 molecule converted
norwid at carnot2:~/Desktop$

Starting .cif, successfully converted .sdf and modified bash script,
each appended by .txt to pass the email, are provided as attachment to
this email.

With best regards,

Norwid Behrnd

 ---- 8>< ---- md5sum ---- ---- attached file ----
d5dac2ef4c96a1c852e34c58e052c48b  1501905.cif.txt
5946d1cd9694511d76007cd3c9458cb5  so.sdf.txt
1daf86169048b51a20ef808805569b6c  molcif2sdf_modified_line_114.txt
 ----

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From antanas.vaitkus90 at gmail.com  Fri May  8 16:28:39 2020
From: antanas.vaitkus90 at gmail.com (Antanas Vaitkus)
Date: Fri, 8 May 2020 16:28:39 +0300
Subject: [Cod-bugs] update suggest cod-tools, bash script molcif2sdf
In-Reply-To: <20200507212047.4170382e@Carnot>
References: <20200507212047.4170382e.ref@Carnot>
 <20200507212047.4170382e@Carnot>
Message-ID: <CALHYoX6s06Y+Y7vX2Ux-VxmnsNR0KHU+dadjJeW5TmFB+TwPzg@mail.gmail.com>

Dear Norwid,

thank you for the report. It seems strange that the script did not work on
your system, since 'babel' is an old version of 'obabel' [1] which still
comes
packaged with the Debian 10 installation of the 'openbabel' package [2].

However, I do agree with your suggestion to replace 'babel' with 'obabel'
since the same approach is also suggested by the openbabel developers [2].
This change will be included in the next release of 'cod-tools'.

[1] https://openbabel.org/docs/dev/Command-line_tools/babel.html
[2] https://packages.debian.org/buster/openbabel

Sincerely,
Antanas

On Thu, 7 May 2020 at 22:21, Norwid Behrnd <nbehrnd at yahoo.com> wrote:

> Dear Ladies and Gentlemen,
>
> based on an observation I would like to suggest an update of bash
> script molcif2sdf (last public edit by 2019-12-06) at line #114; namely,
> the substitution of ?babel? by ?obabel?
>
>
> During a session of Linux Debian 10, backed by openbabel (release
> 3.0.0), I aimed for the conversion of file 1501905.cif into a .sdf
> suitable for DataWarrior with cod-tools' codcif2sdf.  The conversion
> failed and indicated bash script molcif2sdf as possible cause:
>
> norwid at carnot2:~/Desktop$ codcif2sdf 1501905.cif
> /usr/bin/cif_molecule: 1501905.cif data_1501905: WARNING, multiplicity
> ratios are given instead of multiplicities for 61 atoms -- taking
> calculated values.
> /usr/bin/molcif2sdf: 114: babel: not found
> norwid at carnot2:~/Desktop$ codcif2sdf --version
> cod-tools version 2.10
>
>
> A fresh re-installation from Debian's testing repositories did not
> improve the situation, by label they are the same as the tools offered
> by your page as tar.gz.  Tentatively, I substituted ?babel? by ?obabel?
> in line #114 of molcif2sdf and found obtained the .sdf as expected.
>
> norwid at carnot2:~/Desktop$ codcif2sdf 1501905.cif > so.sdf
> /usr/bin/cif_molecule: 1501905.cif data_1501905: WARNING, multiplicity
> ratios are given instead of multiplicities for 61 atoms -- taking
> calculated values. 1 molecule converted
> norwid at carnot2:~/Desktop$
>
> Starting .cif, successfully converted .sdf and modified bash script,
> each appended by .txt to pass the email, are provided as attachment to
> this email.
>
> With best regards,
>
> Norwid Behrnd
>
>  ---- 8>< ---- md5sum ---- ---- attached file ----
> d5dac2ef4c96a1c852e34c58e052c48b  1501905.cif.txt
> 5946d1cd9694511d76007cd3c9458cb5  so.sdf.txt
> 1daf86169048b51a20ef808805569b6c  molcif2sdf_modified_line_114.txt
>  ----
>
> --
> This message has been scanned for viruses and
> dangerous content by MailScanner, 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,
PhD student at Vilnius University Institute of Biotechnology,
room V325, Saul?tekio al. 7,
LT-10257 Vilnius, Lithuania

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