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Re: Questions about CIF files

  • Subject: Re: Questions about CIF files
  • From: Brian McMahon via cif-developers <cif-developers@xxxxxxxxxxxxxxxx>
  • Date: Tue, 27 May 2025 11:11:59 +0100
  • Cc: Brian McMahon <bm@xxxxxxxx>
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  • In-Reply-To: <[email protected]>
  • References: <[email protected]>
Hello Sébastien
Welcome to the cif-developers list. It is often quiet around here, but Iam hoping to provoke some more chat in the near future as I am workingon a survey of CIF software for the forthcoming new edition ofInternational Tables Volume G.
I will leave your major question of interpretation for others moreknowledgeable to reply to, but in response to:
> would you know what to do to add> *atomes* to the visualization tools that can read CIF files,> on this page: https://www.iucr.org/resources/cif/software
I have added an entry for *atomes*. Sometimes it takes a little whilefor the revised page to show up because of server caching behaviour,but you should be able to preview the updated page athttps://www.iucr.org/resources/cif/software/_recache
I would also encourage you to add the program to the more generalsoftware catalogue that the IUCr maintains. You can do this bycompleting the web formhttp://www.iucr.org/resources/other-directories/software/addnewsoftwareentry


Best regardsBrian_________________________________________________________________________Brian McMahonInternational Union of Crystallography (retired)5 Abbey Square, Chester CH1 2HU, England            e-mail:  [email protected]


On 27/05/2025 10:54, Sébastien Le Roux via cif-developers wrote:> Hello everyone,> my name is Sébastien Le Roux: https://www.ipcms.fr/sebastien-le-roux/> I am the developer of the *atomes* software: https://atomes.ipcms.fr/> Among other things *atomes* can be used to read CIF files, and recently> a co-worker of mine> came across an example case that got me thinking, and I would really> appreciate your advise to know what to do.> > Here is the paper, and the corresponding CIF file I am asking your> opinion about:> >  https://journals.iucr.org/paper?S0108768105034014> > The CIF contains several set of atomic coordinates, that corresponds to> a chemical reaction,> that is a transformation of configuration of a molecule in the same> crystalline structure, space group, etc.> Each configuration describing a step in this chemical reaction, with the> proportion of each conformation> being described by the occupancy field, or at least that is what I> understand and want to figure out.> I would like to ask you opinion to know I understand this correctly.> Assuming that is correct and if I consider the CIF file as as trajectory> describing the chemical reaction,> then to build this trajectory, for each set of atomic coordinates, I> would need to: >  - build a crystal respecting the proportion (occupancy) of each> conformation>  - build a (super)crystal large enough to so that even the lowest> occupancy would lead to a cell being filled.>  - ensure that the size of the crystal is the same for each step, and> therefore that the lowest occupancy>  in the overall CIF file dictate the size of the final crystal.> > I would really appreciate your opinion of this, since I am not familiar> with this kind of CIF files.> Is this interpretation based on the occupancy field correct ?> If that is the case then is there any other information in the CIF file> that would help me separate atomic coordinates other than the occupancy ?> Also it this type of CIF file common ? (so far I tried unsuccessfully to> find other examples to verify my hypothesis).> > Finally, and on a different subject, would you know what to do to add> *atomes* to the visualization tools that can read CIF files,> on this page: https://www.iucr.org/resources/cif/software> > Thanks in advance for your help.> Best regards.> > Sébastien Le Roux> > -- > ===========================================================> Dr. Sébastien Le Roux> Ingénieur de Recherche CNRS> Institut de Physique et Chimie des Matériaux de Strasbourg> Département des Matériaux Organiques> 23, rue du Loess> BP 43> F-67034 Strasbourg Cedex 2, France> E-mail: [email protected]> Webpage: https://www.ipcms.fr/sebastien-le-roux/> ATOMES project: https://atomes.ipcms.fr/> RINGS project: http://rings-code.sourceforge.io/> ISAACS project: http://isaacs.sourceforge.io/> Phone: +33 3 88 10 71 58> ===========================================================> > > _______________________________________________> cif-developers mailing list> [email protected]> https://mailman.iucr.org/cgi-bin/mailman/listinfo/cif-developers_______________________________________________cif-developers mailing [email protected]https://mailman.iucr.org/cgi-bin/mailman/listinfo/cif-developers

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