From andrius.merkys at gmail.com Mon Oct 16 14:13:36 2017 From: andrius.merkys at gmail.com (Andrius Merkys) Date: Mon, 16 Oct 2017 14:13:36 +0300 Subject: [Cod-bugs] About .hsrdb In-Reply-To: References: Message-ID: Dear Antonio, CODSeptember2011.hsrdb (in http://www.crystallography.net/archives/2011/PANalytical/) apparently is an SQLite3 database, however, it is generated with proprietary software by PANalytical (http://www.panalytical.com/Xray-diffraction-software/HighScore.htm). Therefore, I advise you to contact them concerning their file structure. Hope this helps, Andrius On 2017.10.10 22:00, Nelcione Carvalho wrote: > Good afternoon. > > I am a young researcher from Brazil. I work with X-ray diffraction, > developing Rietveld refinement software in C ++, among others. > > I was interested in knowing the structure of the .hsrdb file with the > crystal structures database. > > Objective To develop software in C ++ to obtain an .hsrdb file from > the .cif files for easy identification of phases. > -- Andrius Merkys PhD student at Vilnius University Institute of Biotechnology, Saul?tekio al. 7, room V325 LT-10257 Vilnius, Lithuania From rmarti at wustl.edu Tue Oct 17 19:01:55 2017 From: rmarti at wustl.edu (Marti, Robert) Date: Tue, 17 Oct 2017 16:01:55 +0000 Subject: [Cod-bugs] Aluminum Chloride Structure Message-ID: To whom it may concern, I was trying to look at the information card for aluminum chloride (1010563) and there are no atoms. I copied and pasted a screen shot of the visualizer. Maybe portions of this file were accidentally erased or corrupted over time? [cid:6c82a025-2ad4-488c-9390-51ed79dd72d0] Thank you, Robert Marti -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: pastedImage.png Type: image/png Size: 82609 bytes Desc: pastedImage.png URL: From andrius.merkys at gmail.com Wed Oct 18 08:53:43 2017 From: andrius.merkys at gmail.com (Andrius Merkys) Date: Wed, 18 Oct 2017 08:53:43 +0300 Subject: [Cod-bugs] Aluminum Chloride Structure In-Reply-To: References: Message-ID: <85b8bc68-b9b3-d3bf-7c7d-9b8aa75337c2@gmail.com> Dear Robert, entry 1010563 seems to be of a structure from 1930 article (http://onlinelibrary.wiley.com/doi/10.1002/zaac.19301930123/abstract), whose coordinates had not yet been added to the CIF file. There are not many of such structures in the COD, but they are marked as not having coordinates (bottom of the table 'Structure parameters' in http://crystallography.net/cod/1010563.html reads "Has coordinates: No"). Therefore, such entries are exceptions, but are normal. I have just added the coordinates from the original publication to 1010563. Please check whether they seem reasonable. Best wishes, Andrius On 2017.10.17 19:01, Marti, Robert wrote: > > To whom it may concern, > > > ? ? ? I was trying to look at the information card for aluminum > chloride (1010563) and there are no atoms. I copied and pasted a > screen shot of the visualizer. Maybe portions of this file were > accidentally erased or corrupted over time? > > > > > Thank you, > > Robert Marti > > > > _______________________________________________ > Cod-bugs mailing list > Cod-bugs at lists.crystallography.net > http://lists.crystallography.net/cgi-bin/mailman/listinfo/cod-bugs -- Andrius Merkys PhD student at Vilnius University Institute of Biotechnology, Saul?tekio al. 7, room V325 LT-10257 Vilnius, Lithuania -------------- next part -------------- An HTML attachment was scrubbed... URL: From rmarti at wustl.edu Wed Oct 18 17:28:21 2017 From: rmarti at wustl.edu (Marti, Robert) Date: Wed, 18 Oct 2017 14:28:21 +0000 Subject: [Cod-bugs] Aluminum Chloride Structure In-Reply-To: <85b8bc68-b9b3-d3bf-7c7d-9b8aa75337c2@gmail.com> References: , <85b8bc68-b9b3-d3bf-7c7d-9b8aa75337c2@gmail.com> Message-ID: Dear Andrius, Thank you very much for the quick response and updated file! I do have one more question if you don't mind answering it. A hexahydrated version of this crystal structure is on the COD, however, it doesn't look like the hydrogens are in the file. Here is the link to the 3D viewer, http://crystallography.net/cod/1011008.html I assume the structure was determined using XRD data, where hydrogen positions can't really be resolved. So maybe there isn't enough information to do this. Just thought I would check with you to see. (I don't have access to that journal, otherwise I would check to see if it was XRD. Given that it was in 1934, it is probably a safe bet.) Thank you, Robert ________________________________ From: Andrius Merkys Sent: Wednesday, October 18, 2017 12:53:43 AM To: Marti, Robert; cod-bugs at lists.crystallography.net Subject: Re: [Cod-bugs] Aluminum Chloride Structure Dear Robert, entry 1010563 seems to be of a structure from 1930 article (http://onlinelibrary.wiley.com/doi/10.1002/zaac.19301930123/abstract), whose coordinates had not yet been added to the CIF file. There are not many of such structures in the COD, but they are marked as not having coordinates (bottom of the table 'Structure parameters' in http://crystallography.net/cod/1010563.html reads "Has coordinates: No"). Therefore, such entries are exceptions, but are normal. I have just added the coordinates from the original publication to 1010563. Please check whether they seem reasonable. Best wishes, Andrius On 2017.10.17 19:01, Marti, Robert wrote: To whom it may concern, I was trying to look at the information card for aluminum chloride (1010563) and there are no atoms. I copied and pasted a screen shot of the visualizer. Maybe portions of this file were accidentally erased or corrupted over time? [cid:part3.5F1EED67.DEE71657 at gmail.com] Thank you, Robert Marti _______________________________________________ Cod-bugs mailing list Cod-bugs at lists.crystallography.net http://lists.crystallography.net/cgi-bin/mailman/listinfo/cod-bugs -- Andrius Merkys PhD student at Vilnius University Institute of Biotechnology, Saul?tekio al. 7, room V325 LT-10257 Vilnius, Lithuania -------------- next part -------------- An HTML attachment was scrubbed... URL: From andrius.merkys at gmail.com Wed Oct 18 17:43:56 2017 From: andrius.merkys at gmail.com (Andrius Merkys) Date: Wed, 18 Oct 2017 17:43:56 +0300 Subject: [Cod-bugs] Aluminum Chloride Structure In-Reply-To: References: <85b8bc68-b9b3-d3bf-7c7d-9b8aa75337c2@gmail.com> Message-ID: <13e78ba3-6639-9978-7c11-9506455cc3ac@gmail.com> Dear Robert, I also assume that hydrogen positions were not resolved in the case of entry 1011008. I don't have access to the original paper neither, furthermore, my German is poor :) However, in CIF file it is specified that O atom has two attached hydrogen atoms (see _atom_site_attached_hydrogens data item, which is used in cases like this). Therefore, I am quite sure that presence of hydrogen atoms was assumed by authors, but, as said, nothing more than their attachment site was known for sure by authors. Best wishes, Andrius On 2017.10.18 17:28, Marti, Robert wrote: > > Dear Andrius, > > > ? ? ? Thank you very much for the quick response and updated file! I > do have one more question if you don't mind answering it. A > hexahydrated version of this crystal structure is on the COD, however, > it doesn't look like the hydrogens are in the file. Here is the link > to the 3D viewer,?http://crystallography.net/cod/1011008.html > > ? ? ? I assume the structure was determined using XRD?data, where > hydrogen positions can't really be resolved. So maybe there isn't > enough information to do this. Just thought I would check with you to > see. (I don't have access to that journal, otherwise I would check to > see if it was XRD. Given that it was in 1934, it is probably a safe bet.) > > > Thank you, > > Robert > > ------------------------------------------------------------------------ > *From:* Andrius Merkys > *Sent:* Wednesday, October 18, 2017 12:53:43 AM > *To:* Marti, Robert; cod-bugs at lists.crystallography.net > *Subject:* Re: [Cod-bugs] Aluminum Chloride Structure > ? > > Dear Robert, > > > entry 1010563 seems to be of a structure from 1930 article > (http://onlinelibrary.wiley.com/doi/10.1002/zaac.19301930123/abstract), > whose coordinates had not yet been added to the CIF file. There are > not many of such structures in the COD, but they are marked as not > having coordinates (bottom of the table 'Structure parameters' in > http://crystallography.net/cod/1010563.html reads "Has coordinates: > No"). Therefore, such entries are exceptions, but are normal. > > > I have just added the coordinates from the original publication to > 1010563. Please check whether they seem reasonable. > > > Best wishes, > Andrius > > > On 2017.10.17 19:01, Marti, Robert wrote: >> >> To whom it may concern, >> >> >> ? ? ? I was trying to look at the information card for aluminum >> chloride (1010563) and there are no atoms. I copied and pasted a >> screen shot of the visualizer. Maybe portions of this file were >> accidentally erased or corrupted over time? >> >> >> >> >> Thank you, >> >> Robert Marti >> >> >> >> _______________________________________________ >> Cod-bugs mailing list >> Cod-bugs at lists.crystallography.net >> http://lists.crystallography.net/cgi-bin/mailman/listinfo/cod-bugs > > -- > Andrius Merkys > PhD student at Vilnius University Institute of Biotechnology, Saul?tekio al. 7, room V325 > LT-10257 Vilnius, Lithuania -- Andrius Merkys PhD student at Vilnius University Institute of Biotechnology, Saul?tekio al. 7, room V325 LT-10257 Vilnius, Lithuania -------------- next part -------------- An HTML attachment was scrubbed... URL: From rmarti at wustl.edu Wed Oct 18 17:52:40 2017 From: rmarti at wustl.edu (Marti, Robert) Date: Wed, 18 Oct 2017 14:52:40 +0000 Subject: [Cod-bugs] Aluminum Chloride Structure In-Reply-To: <13e78ba3-6639-9978-7c11-9506455cc3ac@gmail.com> References: <85b8bc68-b9b3-d3bf-7c7d-9b8aa75337c2@gmail.com> , <13e78ba3-6639-9978-7c11-9506455cc3ac@gmail.com> Message-ID: Dear Andrius, Hahaha, yeah, my German is also pretty sub-par! Thank you again for the quick response. I thought that might be the case, but it never hurts to check. Have a great rest of the day! Best regards, Robert ________________________________ From: Andrius Merkys Sent: Wednesday, October 18, 2017 9:43:56 AM To: Marti, Robert Cc: cod-bugs at lists.crystallography.net Subject: Re: [Cod-bugs] Aluminum Chloride Structure Dear Robert, I also assume that hydrogen positions were not resolved in the case of entry 1011008. I don't have access to the original paper neither, furthermore, my German is poor :) However, in CIF file it is specified that O atom has two attached hydrogen atoms (see _atom_site_attached_hydrogens data item, which is used in cases like this). Therefore, I am quite sure that presence of hydrogen atoms was assumed by authors, but, as said, nothing more than their attachment site was known for sure by authors. Best wishes, Andrius On 2017.10.18 17:28, Marti, Robert wrote: Dear Andrius, Thank you very much for the quick response and updated file! I do have one more question if you don't mind answering it. A hexahydrated version of this crystal structure is on the COD, however, it doesn't look like the hydrogens are in the file. Here is the link to the 3D viewer, http://crystallography.net/cod/1011008.html I assume the structure was determined using XRD data, where hydrogen positions can't really be resolved. So maybe there isn't enough information to do this. Just thought I would check with you to see. (I don't have access to that journal, otherwise I would check to see if it was XRD. Given that it was in 1934, it is probably a safe bet.) Thank you, Robert ________________________________ From: Andrius Merkys Sent: Wednesday, October 18, 2017 12:53:43 AM To: Marti, Robert; cod-bugs at lists.crystallography.net Subject: Re: [Cod-bugs] Aluminum Chloride Structure Dear Robert, entry 1010563 seems to be of a structure from 1930 article (http://onlinelibrary.wiley.com/doi/10.1002/zaac.19301930123/abstract), whose coordinates had not yet been added to the CIF file. There are not many of such structures in the COD, but they are marked as not having coordinates (bottom of the table 'Structure parameters' in http://crystallography.net/cod/1010563.html reads "Has coordinates: No"). Therefore, such entries are exceptions, but are normal. I have just added the coordinates from the original publication to 1010563. Please check whether they seem reasonable. Best wishes, Andrius On 2017.10.17 19:01, Marti, Robert wrote: To whom it may concern, I was trying to look at the information card for aluminum chloride (1010563) and there are no atoms. I copied and pasted a screen shot of the visualizer. Maybe portions of this file were accidentally erased or corrupted over time? [cid:part3.5F1EED67.DEE71657 at gmail.com] Thank you, Robert Marti _______________________________________________ Cod-bugs mailing list Cod-bugs at lists.crystallography.net http://lists.crystallography.net/cgi-bin/mailman/listinfo/cod-bugs -- Andrius Merkys PhD student at Vilnius University Institute of Biotechnology, Saul?tekio al. 7, room V325 LT-10257 Vilnius, Lithuania -- Andrius Merkys PhD student at Vilnius University Institute of Biotechnology, Saul?tekio al. 7, room V325 LT-10257 Vilnius, Lithuania -------------- next part -------------- An HTML attachment was scrubbed... URL: From grazulis at ibt.lt Thu Oct 19 10:13:00 2017 From: grazulis at ibt.lt (=?UTF-8?Q?Saulius_Gra=c5=beulis?=) Date: Thu, 19 Oct 2017 10:13:00 +0300 Subject: [Cod-bugs] Aluminum Chloride Structure In-Reply-To: <85b8bc68-b9b3-d3bf-7c7d-9b8aa75337c2@gmail.com> References: <85b8bc68-b9b3-d3bf-7c7d-9b8aa75337c2@gmail.com> Message-ID: <08dbaa8f-8b77-d725-80b3-4d99eb72e2be@ibt.lt> Dear Andrius, dear Robert! thanks for taking care about this entry and for finding the coordinates! On 2017-10-18 08:53, Andrius Merkys wrote: > entry 1010563 seems to be of a structure from 1930 article > (http://onlinelibrary.wiley.com/doi/10.1002/zaac.19301930123/abstract), > whose coordinates had not yet been added to the CIF file. There are not > many of such structures in the COD, but they are marked as not having > coordinates (bottom of the table 'Structure parameters' in > http://crystallography.net/cod/1010563.html reads "Has coordinates: > No"). Therefore, such entries are exceptions, but are normal. > > I have just added the coordinates from the original publication to > 1010563. Please check whether they seem reasonable. The coordinates seem reasonable but the space group is definitely not P1 -- there are gaps in Al layers, and the structure clearly has at least a 3-fold axis (see attached screen-shots). Robert, please do not use the COD entry 1010563 untill we fix the space group (hopefully we do that today). Regards, Saulius -- Dr. Saulius Gra?ulis Vilnius University Institute of Biotechnology, Saul?tekio al. 7 LT-10257 Vilnius, Lietuva (Lithuania) fax: (+370-5)-2234367 / phone (office): (+370-5)-2234353 mobile: (+370-684)-49802, (+370-614)-36366 -------------- next part -------------- A non-text attachment was scrubbed... Name: Screenshot from 2017-10-19 10-11-37.png Type: image/png Size: 197661 bytes Desc: not available URL: -------------- next part -------------- A non-text attachment was scrubbed... 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