From david at crystalmaker.com Tue Jul 18 17:43:33 2017 From: david at crystalmaker.com (David Palmer) Date: Tue, 18 Jul 2017 15:43:33 +0100 Subject: [Cod-bugs] Invalid CIFs for LiNbO3 Message-ID: Dear Sir/Madam, The following CIF entries for LiNbO3 are invalid:- 2101176 - 2101185 These files violate the CIF standard by failing to include any general-equivalent positions - as is required in the CIF file specification. Instead, the files simply give a vague spacegroup symbol (NOTE: there is no agreed syntax for plain-text spacegroup symbols, so authors should NEVER rely on a plain-text spacegroup string in a CIF file.) For reference, the missing general equivalent positions would be as given in the following output from CrystalMaker X (*):- loop_ _symmetry_equiv_pos_as_xyz '+x,+y,+z' '-y,+x-y,+z' '-x+y,-x,+z' '-y,-x,1/2+z' '-x+y,+y,1/2+z' '+x,+x-y,1/2+z' '2/3+x,1/3+y,1/3+z' '1/3+x,2/3+y,2/3+z' '2/3-y,1/3+x-y,1/3+z' '1/3-y,2/3+x-y,2/3+z' '2/3-x+y,1/3-x,1/3+z' '1/3-x+y,2/3-x,2/3+z' '2/3-y,1/3-x,5/6+z' '1/3-y,2/3-x,1/6+z' '2/3-x+y,1/3+y,5/6+z' '1/3-x+y,2/3+y,1/6+z' '2/3+x,1/3+x-y,5/6+z' '1/3+x,2/3+x-y,1/6+z' I hope this helps. Best wishes, David Palmer (*) CrystalMaker X is a user-funded project to develop the world?s best software for crystal and molecular structures. We receive no government funding, salaries, research grants or external sponsorship: all our software is funded by our users. Pure, transparent, honest. The only viable option for long-term development and support. From antanas.vaitkus90 at gmail.com Tue Jul 18 20:30:49 2017 From: antanas.vaitkus90 at gmail.com (Antanas Vaitkus) Date: Tue, 18 Jul 2017 20:30:49 +0300 Subject: [Cod-bugs] Invalid CIFs for LiNbO3 In-Reply-To: References: Message-ID: Dear David Palmer, thank you for notifying us of this issue. I have updated the symmetry information in entries 2101175-2101185 (entry 2101175 had the same problem as well). The issue seems to have originated upstream in the supplementary material of the original publication. Most likely the files were ingested into the database in the early days of the COD before the rigorous automated checks were implemented. Currently, all newly added structures are required to have the symmetry operation loop. There might still be some files that are missing the symmetry operation information, but these will be located and tended to once enough resources can be allocated towards this task. Please let us know if you spot any more inconsistencies in the COD. Sincerely, Antanas Vaitkus 2017-07-18 17:43 GMT+03:00 David Palmer : > Dear Sir/Madam, > > The following CIF entries for LiNbO3 are invalid:- > > 2101176 - 2101185 > > These files violate the CIF standard by failing to include any > general-equivalent positions - as is required in the CIF file > specification. Instead, the files simply give a vague spacegroup symbol > (NOTE: there is no agreed syntax for plain-text spacegroup symbols, so > authors should NEVER rely on a plain-text spacegroup string in a CIF file.) > > For reference, the missing general equivalent positions would be as given > in the following output from CrystalMaker X (*):- > > loop_ > _symmetry_equiv_pos_as_xyz > '+x,+y,+z' > '-y,+x-y,+z' > '-x+y,-x,+z' > '-y,-x,1/2+z' > '-x+y,+y,1/2+z' > '+x,+x-y,1/2+z' > '2/3+x,1/3+y,1/3+z' > '1/3+x,2/3+y,2/3+z' > '2/3-y,1/3+x-y,1/3+z' > '1/3-y,2/3+x-y,2/3+z' > '2/3-x+y,1/3-x,1/3+z' > '1/3-x+y,2/3-x,2/3+z' > '2/3-y,1/3-x,5/6+z' > '1/3-y,2/3-x,1/6+z' > '2/3-x+y,1/3+y,5/6+z' > '1/3-x+y,2/3+y,1/6+z' > '2/3+x,1/3+x-y,5/6+z' > '1/3+x,2/3+x-y,1/6+z' > > I hope this helps. > > Best wishes, > > David Palmer > > > (*) CrystalMaker X is a user-funded project to develop the world?s best > software for crystal and molecular structures. We receive no government > funding, salaries, research grants or external sponsorship: all our > software is funded by our users. Pure, transparent, honest. The only viable > option for long-term development and support. > _______________________________________________ > 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 -------------- next part -------------- An HTML attachment was scrubbed... URL: From antanas.vaitkus90 at gmail.com Wed Jul 19 11:49:15 2017 From: antanas.vaitkus90 at gmail.com (Antanas Vaitkus) Date: Wed, 19 Jul 2017 11:49:15 +0300 Subject: [Cod-bugs] Fwd: Invalid CIFs for LiNbO3 In-Reply-To: <86D8DEB9-7E73-4143-9CA3-4D897D552C52@crystalmaker.com> References:

<86D8DEB9-7E73-4143-9CA3-4D897D552C52@crystalmaker.com> Message-ID: ---------- Forwarded message ---------- From: David Palmer Date: 2017-07-19 11:39 GMT+03:00 Subject: Re: [Cod-bugs] Invalid CIFs for LiNbO3 To: Antanas Vaitkus Dear Antanas, Thanks for your prompt help - much appreciated! Best wishes, David On 18 Jul, 2017, at 18:30, Antanas Vaitkus wrote: Dear David Palmer, thank you for notifying us of this issue. I have updated the symmetry information in entries 2101175-2101185 (entry 2101175 had the same problem as well). The issue seems to have originated upstream in the supplementary material of the original publication. Most likely the files were ingested into the database in the early days of the COD before the rigorous automated checks were implemented. Currently, all newly added structures are required to have the symmetry operation loop. There might still be some files that are missing the symmetry operation information, but these will be located and tended to once enough resources can be allocated towards this task. Please let us know if you spot any more inconsistencies in the COD. _______________________________________________________________ Dr David C Palmer, Managing Director CrystalMaker Software Ltd Centre for Innovation & Enterprise Oxford University Begbroke Science Park Woodstock Road, Begbroke, Oxfordshire, OX5 1PF, UK Voice: +44 1865-854804 <+44%201865%20854804> Fax: +44 1865-854805 <+44%201865%20854805> Website: http://www.crystalmaker.com CrystalMaker Software Ltd is a pioneer in interactive scientific multimedia and learning technologies. We specialize in advanced visualization of crystal structures and their diffraction patterns. Company registered in England, no. 4824441 _______________________________________________________________ -- Antanas Vaitkus, PhD student at Vilnius University Institute of Biotechnology, room V325, Saul?tekio al. 7, LT-10257 Vilnius, Lithuania -------------- next part -------------- An HTML attachment was scrubbed... URL: From Neel.D at shell.com Tue Jul 18 13:01:14 2017 From: Neel.D at shell.com (Neel.D at shell.com) Date: Tue, 18 Jul 2017 10:01:14 +0000 Subject: [Cod-bugs] FW: Question about published zeolites data In-Reply-To: References: <1955D88C78024643BED523E47BEA8B12A84DE8@SEACMW-S-53442.europe.shell.com> <2e684d8df8a146c285a4fd2a74c8e099@exch1-mel.nexus.csiro.au>

Message-ID: Hi, We are working on a project about zeolites for their role in gas separation. We are analyzing a data set published by Dr. Aaron Thornton from CSIRO. We are trying to augment the dataset with more information about the chemistry of the zeolites by using the structures of the zeolites. You can read the full purpose in the previous emails. As I was looking through the PCOD database, I discovered that several of the zeolites from Dr. Thornton's dataset were missing from the PCOD database: 70 of them to be exact. I am attaching the missing zeolites in a text file. We were wondering if you could let us know why these zeolites are missing or how we can obtain more information about them. Thanks, Neel Das, Michal Gala From: Aaron.Thornton at csiro.au [mailto:Aaron.Thornton at csiro.au] Sent: Tuesday, July 18, 2017 4:37 AM To: D, Neel PTIN-PTI/CT ; G, Michal PTIN-PTI/CT Subject: RE: Question about published zeolites data Hi Neel and Michal, Sounds like an interesting project. I just checked and you are right. There are missing structures on the website. I'm not sure why. You will have to contact the owners at: cod-bugs at ibt.lt I'd be interested to hear their response. Keep in touch. Best wishes, Aaron From: Neel.D at shell.com [mailto:Neel.D at shell.com] Sent: Friday, 7 July 2017 6:42 PM To: Thornton, Aaron (Manufacturing, Clayton NHC) >; Michal.G at shell.com Subject: RE: Question about published zeolites data Hi Dr. Thornton, I have a follow up question about this. I started checking the Zeolites from the Zeolites dataset, and the last 21 of the PCOD and last 49 of the h Zeolites are not in this PCOD database, and I am wondering if you know why. The numbers are attached. Just some context for this project: Michal and I are MIT students who are doing research at Shell this summer and we are currently looking at Zeolites for their role in gas separation. We are hoping to augment the dataset with more information about the chemistry of the zeolites. Then we hope to gain more insight by analyzing the data with machine learning algorithms. Thanks, Neel Das, Michal Gala From: Aaron.Thornton at csiro.au [mailto:Aaron.Thornton at csiro.au] Sent: Thursday, July 06, 2017 4:44 AM To: G, Michal PTIN-PTI/CT > Cc: D, Neel PTIN-PTI/CT > Subject: RE: Question about published zeolites data Hi Michael, Thanks for your interest in our work. You can search the PCOD database here: http://www.crystallography.net/pcod/ Just use the text search with the PCOD number that you mention below. Best wishes, Aaron From: Michal.G at shell.com [mailto:Michal.G at shell.com] Sent: Tuesday, 4 July 2017 3:05 PM To: Thornton, Aaron (Manufacturing, Clayton NHC) > Cc: Neel.D at shell.com Subject: Question about published zeolites data Dear Dr. Thornton, We are doing research on zeolites at the Shell Technology Center in Bangalore and recently started working a dataset from your publication "Towards computational design of zeolite catalysts for CO2 reduction". We are considering augmenting the dataset with information on the chemical properties of the zeolites studied and to that end we want to find the structures of zeolites from the dataset. Of the three types of labels we managed to identify the meaning of the ones with three-letter acronyms but we can't find any information on zeolites under the names starting with 'h' (e.g. h8195254) or 'PCOD' (e.g. PCOD8287257). Could you give us any guidance as it comes to assigning these zeolites to their structures? Best regards, Michal Gala, Neel Das -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- An embedded and charset-unspecified text was scrubbed... Name: invalid_h.txt URL: -------------- next part -------------- An embedded and charset-unspecified text was scrubbed... Name: invalid_PCOD.txt URL: