From klaus-dieter.liss at gtiit.edu.cn Mon Jan 8 10:05:58 2018 From: klaus-dieter.liss at gtiit.edu.cn (Klaus-Dieter Liss - GTIIT) Date: Mon, 8 Jan 2018 16:05:58 +0800 Subject: [Cod-bugs] change of email address Message-ID: <99555979-31a3-20f5-f66e-b1055b0ec794@gtiit.edu.cn> Hello, I have changed my email address from kdl at ansto.gov.au to liss at kdliss.de (preferred) and kdl at gtiit.edu.cn how to update in COD? Klaus-Dieter -- -- Prof. Dr. Klaus-Dieter Liss Materials and Engineering Science Program Guangdong Technion - Israel Institute of Technology Materials and Quantum Beams ? China Center of Excellence 241 Daxue Lu, Jinping Qu Shantou 515063 Guangdong, China M: klaus-dieter.liss at gtiit.edu.cn T: +86-0754-88077102 H: +86-136-7612-7052 S: 667052 W: http://www.gtiit.edu.cn/en/ W: http://www.gtiit.edu.cn/en/viewStaff.aspx?staffNo=9 R: Administration Building A324 From antanas.vaitkus90 at gmail.com Mon Jan 8 15:01:59 2018 From: antanas.vaitkus90 at gmail.com (Antanas Vaitkus) Date: Mon, 8 Jan 2018 15:01:59 +0200 Subject: [Cod-bugs] change of email address In-Reply-To: <99555979-31a3-20f5-f66e-b1055b0ec794@gtiit.edu.cn> References: <99555979-31a3-20f5-f66e-b1055b0ec794@gtiit.edu.cn> Message-ID: Dear Klaus-Dieter Liss, the e-mail address is updated the same way as all the other depositor details: 1. Go to the main page and click the "Manage depositions" link; 2. Type in Your details and login into the Account Management Interface; 3. Click on the "Change your depositor details" link; 4. Replace Your old e-mail with the new one and press the "Update account details" button. Please let us know if You encounter any difficulties with the outlines process. Sincerely, Antanas Vaitkus 2018-01-08 10:05 GMT+02:00 Klaus-Dieter Liss - GTIIT < klaus-dieter.liss at gtiit.edu.cn>: > Hello, > > I have changed my email address from kdl at ansto.gov.au to liss at kdliss.de > (preferred) and kdl at gtiit.edu.cn > > how to update in COD? > > Klaus-Dieter > > > > -- > -- > Prof. Dr. Klaus-Dieter Liss > Materials and Engineering Science Program > Guangdong Technion - Israel Institute of Technology > Materials and Quantum Beams ? China Center of Excellence > > 241 Daxue Lu, Jinping Qu > Shantou 515063 > Guangdong, China > > M: klaus-dieter.liss at gtiit.edu.cn > T: +86-0754-88077102 > H: +86-136-7612-7052 > S: 667052 > W: http://www.gtiit.edu.cn/en/ > W: http://www.gtiit.edu.cn/en/viewStaff.aspx?staffNo=9 > R: Administration Building A324 > > _______________________________________________ > 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 tim.gruene at psi.ch Mon Jan 8 22:29:33 2018 From: tim.gruene at psi.ch (Tim Gruene) Date: Mon, 8 Jan 2018 21:29:33 +0100 Subject: [Cod-bugs] wrong 'duplicate entry' upon deposition Message-ID: <11842160.7or0m90rPk@vonneumann> Dear maintainers of the COD, today I uploaded 12 CIF files to the COD as one single concatenated CIF. Afterwards I realised that I had forgotten one file during concatenation which I tried to upload right now. This time I received a warning, the additional file was a duplicate of one of my previous files. How can I still upload this extra file? I need to explain the peculiarity of these files: The CIF files refer to DOI 10.1002/chem.201704213. The important parts are the data, which are encoded in the CIFs and available through shredcif. I did solve the structures of the zeolites, but they are of secondary interest. The file that I failed to upload represents the merged data between COD entry 1548620 and 1548621. As the merging included a rescaling with XSCALE, it is not identical to just concatentating the two hkl-files (although probably quite similar). I would appreciate if I could also upload the final CIF-file and provide the COD number to ChemEurJ to provide the links with the online publication. Best regards, Tim Gruene -- -- Paul Scherrer Institut Tim Gruene - persoenlich - OFLC/104 CH-5232 Villigen PSI phone: +41 (0)56 310 5297 GPG Key ID = A46BEE1A -------------- next part -------------- A non-text attachment was scrubbed... Name: signature.asc Type: application/pgp-signature Size: 195 bytes Desc: This is a digitally signed message part. URL: From grazulis at ibt.lt Thu Jan 11 07:59:40 2018 From: grazulis at ibt.lt (=?UTF-8?Q?Saulius_Gra=c5=beulis?=) Date: Thu, 11 Jan 2018 07:59:40 +0200 Subject: [Cod-bugs] Fwd: Cod-bugs post from tim.gruene@psi.ch requires approval In-Reply-To: References: Message-ID: -------- Forwarded Message -------- Subject: Cod-bugs post from tim.gruene at psi.ch requires approval Date: Mon, 08 Jan 2018 22:30:02 +0200 From: cod-bugs-owner at lists.crystallography.net To: cod-bugs-owner at lists.crystallography.net As list administrator, your authorization is requested for the following mailing list posting: List: Cod-bugs at lists.crystallography.net From: tim.gruene at psi.ch Subject: wrong 'duplicate entry' upon deposition Reason: Post by non-member to a members-only list At your convenience, visit: http://lists.crystallography.net/cgi-bin/mailman/admindb/cod-bugs to approve or deny the request. -------------- next part -------------- An embedded message was scrubbed... From: Tim Gruene Subject: wrong 'duplicate entry' upon deposition Date: Mon, 8 Jan 2018 21:29:33 +0100 Size: 3482 URL: -------------- next part -------------- An embedded message was scrubbed... From: cod-bugs-request at lists.crystallography.net Subject: confirm fb23b7992cd4c54784f9e5e39ca0882c32332312 Date: Mon, 08 Jan 2018 22:30:02 +0200 Size: 901 URL: From antanas.vaitkus90 at gmail.com Thu Jan 11 10:43:42 2018 From: antanas.vaitkus90 at gmail.com (Antanas Vaitkus) Date: Thu, 11 Jan 2018 10:43:42 +0200 Subject: [Cod-bugs] wrong 'duplicate entry' upon deposition In-Reply-To: <11842160.7or0m90rPk@vonneumann> References: <11842160.7or0m90rPk@vonneumann> Message-ID: Dear Tim Gruene, sorry for the late response -- Your mail got lost in our spam filter for some reason. Regarding You inquiry, could You please provide the following: 1) COD IDs of the files that were successfully deposited; 2) The CIF file that did not pass the check. Also, did You deposit Your files as "Already published data" or as "Prepublication data"? Sincerely, Antanas Vaitkus 2018-01-08 22:29 GMT+02:00 Tim Gruene : > Dear maintainers of the COD, > > today I uploaded 12 CIF files to the COD as one single concatenated CIF. > Afterwards I realised that I had forgotten one file during concatenation > which > I tried to upload right now. > This time I received a warning, the additional file was a duplicate of one > of > my previous files. How can I still upload this extra file? > > I need to explain the peculiarity of these files: > The CIF files refer to DOI 10.1002/chem.201704213. > > The important parts are the data, which are encoded in the CIFs and > available > through shredcif. I did solve the structures of the zeolites, but they are > of > secondary interest. > > The file that I failed to upload represents the merged data between COD > entry > 1548620 and 1548621. As the merging included a rescaling with XSCALE, it is > not identical to just concatentating the two hkl-files (although probably > quite similar). > > I would appreciate if I could also upload the final CIF-file and provide > the > COD number to ChemEurJ to provide the links with the online publication. > > Best regards, > Tim Gruene > -- > -- > Paul Scherrer Institut > Tim Gruene > - persoenlich - > OFLC/104 > CH-5232 Villigen PSI > phone: +41 (0)56 310 5297 > > GPG Key ID = A46BEE1A > > _______________________________________________ > 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 tim.gruene at psi.ch Thu Jan 11 11:38:48 2018 From: tim.gruene at psi.ch (Tim Gruene) Date: Thu, 11 Jan 2018 10:38:48 +0100 Subject: [Cod-bugs] wrong 'duplicate entry' upon deposition In-Reply-To: References: <11842160.7or0m90rPk@vonneumann> Message-ID: <2883494.b4PG3pVC28@vonneumann> Dear Antanas, thank you very much for your reply! The COD IDs read 1548620 1548621 1548622 1548623 1548624 1548625 1548626 1548627 1548628 1548629 1548630 1548631 all of these were uploaded as one single CIF file. I assume this is the reason why none of them were marked as duplicates. The missing CIF-file, sil1.cif, has been attached. Thank you very much for looking into this. Kind regards, Tim Gruene P.S.: thank you for letting me know about the spam. The reason is probably on my Institute's side. On Thursday, January 11, 2018 10:43:42 AM CET Antanas Vaitkus wrote: > Dear Tim Gruene, > > sorry for the late response -- Your mail got lost in our spam filter for > some reason. > > Regarding You inquiry, could You please provide the following: > 1) COD IDs of the files that were successfully deposited; > 2) The CIF file that did not pass the check. > > Also, did You deposit Your files as "Already published data" or as > "Prepublication data"? > > Sincerely, > Antanas Vaitkus > > 2018-01-08 22:29 GMT+02:00 Tim Gruene : > > Dear maintainers of the COD, > > > > today I uploaded 12 CIF files to the COD as one single concatenated CIF. > > Afterwards I realised that I had forgotten one file during concatenation > > which > > I tried to upload right now. > > This time I received a warning, the additional file was a duplicate of one > > of > > my previous files. How can I still upload this extra file? > > > > I need to explain the peculiarity of these files: > > The CIF files refer to DOI 10.1002/chem.201704213. > > > > The important parts are the data, which are encoded in the CIFs and > > available > > through shredcif. I did solve the structures of the zeolites, but they are > > of > > secondary interest. > > > > The file that I failed to upload represents the merged data between COD > > entry > > 1548620 and 1548621. As the merging included a rescaling with XSCALE, it > > is > > not identical to just concatentating the two hkl-files (although probably > > quite similar). > > > > I would appreciate if I could also upload the final CIF-file and provide > > the > > COD number to ChemEurJ to provide the links with the online publication. > > > > Best regards, > > Tim Gruene > > -- > > -- > > Paul Scherrer Institut > > Tim Gruene > > - persoenlich - > > OFLC/104 > > CH-5232 Villigen PSI > > phone: +41 (0)56 310 5297 > > > > GPG Key ID = A46BEE1A > > > > _______________________________________________ > > Cod-bugs mailing list > > Cod-bugs at lists.crystallography.net > > http://lists.crystallography.net/cgi-bin/mailman/listinfo/cod-bugs -- -- Paul Scherrer Institut Tim Gruene - persoenlich - OFLC/104 CH-5232 Villigen PSI phone: +41 (0)56 310 5297 GPG Key ID = A46BEE1A -------------- next part -------------- A non-text attachment was scrubbed... Name: sil1.cif.zip Type: application/zip Size: 278235 bytes Desc: not available URL: From antanas.vaitkus90 at gmail.com Thu Jan 11 13:01:39 2018 From: antanas.vaitkus90 at gmail.com (Antanas Vaitkus) Date: Thu, 11 Jan 2018 13:01:39 +0200 Subject: [Cod-bugs] wrong 'duplicate entry' upon deposition In-Reply-To: <2883494.b4PG3pVC28@vonneumann> References: <11842160.7or0m90rPk@vonneumann> <2883494.b4PG3pVC28@vonneumann> Message-ID: Dear Tim, you are totally correct about the bulk upload. The duplicate search might be too aggressive sometimes, but You know as they say -- better safe than sorry. I have uploaded Your structure manually as entry 1548658 ( http://www.crystallography.net/cod/1548658.html). I have also added DOI to the other entries so they would be easier to locate. Please let us know if there are any more problems. Sincerely, Antanas Vaitkus 2018-01-11 11:38 GMT+02:00 Tim Gruene : > Dear Antanas, > > thank you very much for your reply! > > The COD IDs read > 1548620 1548621 1548622 1548623 1548624 1548625 1548626 > 1548627 1548628 1548629 1548630 1548631 > > all of these were uploaded as one single CIF file. I assume this is the > reason > why none of them were marked as duplicates. The missing CIF-file, sil1.cif, > has been attached. > > Thank you very much for looking into this. > > Kind regards, > Tim Gruene > > P.S.: thank you for letting me know about the spam. The reason is probably > on > my Institute's side. > > > > On Thursday, January 11, 2018 10:43:42 AM CET Antanas Vaitkus wrote: > > Dear Tim Gruene, > > > > sorry for the late response -- Your mail got lost in our spam filter for > > some reason. > > > > Regarding You inquiry, could You please provide the following: > > 1) COD IDs of the files that were successfully deposited; > > 2) The CIF file that did not pass the check. > > > > Also, did You deposit Your files as "Already published data" or as > > "Prepublication data"? > > > > Sincerely, > > Antanas Vaitkus > > > > 2018-01-08 22:29 GMT+02:00 Tim Gruene : > > > Dear maintainers of the COD, > > > > > > today I uploaded 12 CIF files to the COD as one single concatenated > CIF. > > > Afterwards I realised that I had forgotten one file during > concatenation > > > which > > > I tried to upload right now. > > > This time I received a warning, the additional file was a duplicate of > one > > > of > > > my previous files. How can I still upload this extra file? > > > > > > I need to explain the peculiarity of these files: > > > The CIF files refer to DOI 10.1002/chem.201704213. > > > > > > The important parts are the data, which are encoded in the CIFs and > > > available > > > through shredcif. I did solve the structures of the zeolites, but they > are > > > of > > > secondary interest. > > > > > > The file that I failed to upload represents the merged data between COD > > > entry > > > 1548620 and 1548621. As the merging included a rescaling with XSCALE, > it > > > is > > > not identical to just concatentating the two hkl-files (although > probably > > > quite similar). > > > > > > I would appreciate if I could also upload the final CIF-file and > provide > > > the > > > COD number to ChemEurJ to provide the links with the online > publication. > > > > > > Best regards, > > > Tim Gruene > > > -- > > > -- > > > Paul Scherrer Institut > > > Tim Gruene > > > - persoenlich - > > > OFLC/104 > > > CH-5232 Villigen PSI > > > phone: +41 (0)56 310 5297 > > > > > > GPG Key ID = A46BEE1A > > > > > > _______________________________________________ > > > Cod-bugs mailing list > > > Cod-bugs at lists.crystallography.net > > > http://lists.crystallography.net/cgi-bin/mailman/listinfo/cod-bugs > > -- > -- > Paul Scherrer Institut > Tim Gruene > - persoenlich - > OFLC/104 > CH-5232 Villigen PSI > phone: +41 (0)56 310 5297 > > GPG Key ID = A46BEE1A > -- 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 tim.gruene at psi.ch Fri Jan 12 14:23:16 2018 From: tim.gruene at psi.ch (Tim Gruene) Date: Fri, 12 Jan 2018 13:23:16 +0100 Subject: [Cod-bugs] wrong 'duplicate entry' upon deposition In-Reply-To: References: <11842160.7or0m90rPk@vonneumann> <2883494.b4PG3pVC28@vonneumann> Message-ID: <2102359.JgWcHYMLvn@vonneumann> Dear Antanas, I fully agree, it is better to be safe! Thank you very, very much for finalising my upload, and for adding the DOI to al entries! Best regards, Tim On Thursday, January 11, 2018 1:01:39 PM CET Antanas Vaitkus wrote: > Dear Tim, > > you are totally correct about the bulk upload. The duplicate search might > be too aggressive sometimes, but You know as they say -- better safe than > sorry. > > I have uploaded Your structure manually as entry 1548658 ( > http://www.crystallography.net/cod/1548658.html). > I have also added DOI to the other entries so they would be easier to > locate. > > Please let us know if there are any more problems. > > Sincerely, > Antanas Vaitkus > > 2018-01-11 11:38 GMT+02:00 Tim Gruene : > > Dear Antanas, > > > > thank you very much for your reply! > > > > The COD IDs read > > 1548620 1548621 1548622 1548623 1548624 1548625 1548626 > > 1548627 1548628 1548629 1548630 1548631 > > > > all of these were uploaded as one single CIF file. I assume this is the > > reason > > why none of them were marked as duplicates. The missing CIF-file, > > sil1.cif, > > has been attached. > > > > Thank you very much for looking into this. > > > > Kind regards, > > Tim Gruene > > > > P.S.: thank you for letting me know about the spam. The reason is probably > > on > > my Institute's side. > > > > On Thursday, January 11, 2018 10:43:42 AM CET Antanas Vaitkus wrote: > > > Dear Tim Gruene, > > > > > > sorry for the late response -- Your mail got lost in our spam filter for > > > some reason. > > > > > > Regarding You inquiry, could You please provide the following: > > > 1) COD IDs of the files that were successfully deposited; > > > 2) The CIF file that did not pass the check. > > > > > > Also, did You deposit Your files as "Already published data" or as > > > "Prepublication data"? > > > > > > Sincerely, > > > Antanas Vaitkus > > > > > > 2018-01-08 22:29 GMT+02:00 Tim Gruene : > > > > Dear maintainers of the COD, > > > > > > > > today I uploaded 12 CIF files to the COD as one single concatenated > > > > CIF. > > > > > > Afterwards I realised that I had forgotten one file during > > > > concatenation > > > > > > which > > > > I tried to upload right now. > > > > This time I received a warning, the additional file was a duplicate of > > > > one > > > > > > of > > > > my previous files. How can I still upload this extra file? > > > > > > > > I need to explain the peculiarity of these files: > > > > The CIF files refer to DOI 10.1002/chem.201704213. > > > > > > > > The important parts are the data, which are encoded in the CIFs and > > > > available > > > > through shredcif. I did solve the structures of the zeolites, but they > > > > are > > > > > > of > > > > secondary interest. > > > > > > > > The file that I failed to upload represents the merged data between > > > > COD > > > > entry > > > > 1548620 and 1548621. As the merging included a rescaling with XSCALE, > > > > it > > > > > > is > > > > not identical to just concatentating the two hkl-files (although > > > > probably > > > > > > quite similar). > > > > > > > > I would appreciate if I could also upload the final CIF-file and > > > > provide > > > > > > the > > > > COD number to ChemEurJ to provide the links with the online > > > > publication. > > > > > > Best regards, > > > > Tim Gruene > > > > -- > > > > -- > > > > Paul Scherrer Institut > > > > Tim Gruene > > > > - persoenlich - > > > > OFLC/104 > > > > CH-5232 Villigen PSI > > > > phone: +41 (0)56 310 5297 > > > > > > > > GPG Key ID = A46BEE1A > > > > > > > > _______________________________________________ > > > > Cod-bugs mailing list > > > > Cod-bugs at lists.crystallography.net > > > > http://lists.crystallography.net/cgi-bin/mailman/listinfo/cod-bugs > > > > -- > > -- > > Paul Scherrer Institut > > Tim Gruene > > - persoenlich - > > OFLC/104 > > CH-5232 Villigen PSI > > phone: +41 (0)56 310 5297 > > > > GPG Key ID = A46BEE1A -- -- Paul Scherrer Institut Tim Gruene - persoenlich - OFLC/104 CH-5232 Villigen PSI phone: +41 (0)56 310 5297 GPG Key ID = A46BEE1A -------------- next part -------------- A non-text attachment was scrubbed... Name: signature.asc Type: application/pgp-signature Size: 195 bytes Desc: This is a digitally signed message part. URL: From iborged at gmail.com Fri Jan 12 00:24:29 2018 From: iborged at gmail.com (Ignacio Borge) Date: Fri, 12 Jan 2018 00:24:29 +0200 Subject: [Cod-bugs] Cobalt hydroxide problem. Message-ID: Dear reader, *1*.First I want to thank for this amazing data-base *2*. There is a bug in the cobalt hydroxide file, the hydrogens does not appear (1010267.cif). Every time that I try to open it, appear a cobalt oxide and should be cobalt hydroxide. Thanks Kind regards, -- Ignacio Borge. -------------- next part -------------- An HTML attachment was scrubbed... URL: From antanas.vaitkus90 at gmail.com Fri Jan 12 18:09:42 2018 From: antanas.vaitkus90 at gmail.com (Antanas Vaitkus) Date: Fri, 12 Jan 2018 18:09:42 +0200 Subject: [Cod-bugs] Cobalt hydroxide problem. In-Reply-To: References: Message-ID: Dear Ignacio Borge, thank You for the kind words. However, entry 1010267 does not contain a bug. Since the experiment was conducted quite a while a go (in 1936 to be exact!) the authors simply were not able to determine the hydrogen positions reliably. As a result, only the coordinates of heavy atoms were described in the publication. In situations like these, the hydrogen atoms are sometimes marked using the *_atom_site_attached_hydrogens* data item, i.e. the coordinate loop from entry 1010267: loop_ _atom_site_label _atom_site_type_symbol _atom_site_symmetry_multiplicity _atom_site_Wyckoff_symbol _atom_site_fract_x _atom_site_fract_y _atom_site_fract_z _atom_site_occupancy *_atom_site_attached_hydrogens* _atom_site_calc_flag Co1 Co2+ 1 a 0. 0. 0. 1. *0* d O1 O2- 2 d 0.3333 0.6667 0.22 1. *1* d denotes that the 'O1' atom has 1 attached hydrogen for which explicit coordinates are not provided. Hope this help. Feel free to write if You have any more questions. Sincerely, Antanas Vaitkus 2018-01-12 0:24 GMT+02:00 Ignacio Borge : > Dear reader, > > *1*.First I want to thank for this amazing data-base > > *2*. There is a bug in the cobalt hydroxide file, the hydrogens does not > appear (1010267.cif). Every time that I try to open it, appear a cobalt > oxide and should be cobalt hydroxide. > > Thanks > > Kind regards, > -- > Ignacio Borge. > > > > _______________________________________________ > 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: