From grazulis at ibt.lt Tue Feb 25 08:05:55 2020 From: grazulis at ibt.lt (=?UTF-8?Q?Saulius_Gra=c5=beulis?=) Date: Tue, 25 Feb 2020 08:05:55 +0200 Subject: [Cod-bugs] COD to PDF In-Reply-To: References: Message-ID: <5bb4b818-2243-b800-fe87-49146b3a61b7@ibt.lt> Dear Silvi, thank you for your message. I'll try to answer your questions below, although I need more context for my answers to be more precise. The short answer would be that we maintain *no* links with ICDD PDF entries or any other commercial databases. Commercial databases have restrictive licenses, and we are explicitly forbidden to take any data from them, including their identifiers. This restrictiveness is actually one of the main reasons why the COD was started! On 2020-02-18 21:02, Silvina Di Pietro wrote: > I had a simple question: I am currently using Eva software on my > school's XRD lab. Whenever I match, I get specific COD #. I was > wondering if this # could be "translated" into PDF from the ICDD database. What you mean by ?PDF? in this context? Do you mean a Page Description File from Adobe (PDF), generated by ICDD software for a crystallographic entry, or do you mean a record identifier from the powder Diffraction File (PDF) marketed by ICDD? In both cases the answer would be "no", but for different reasons, and thus the workarounds would be different: - if you want a (nice) page description file (PDF) for a structure, then of course we can not run the ICDD software for you on our servers (the software is proprietary), but you can use your browser to find a particular COD structure easily if you know its COD ID ? either use the COD "Search" page and paste the COD ID into the "Search by COD ID:" field, or construct a stable URI for this structure, e.g. for the COD ID 7239975 it would be: https://www.crystallography.net/cod/7239975.html You can then of course use your browser's "print to file" functionality to produce a PDF file. - if you want a corresponding Powder Diffraction File (PDF) identifier, then you have to search for the structure in the PDF using their provided software for the same material. You will have to own a license for PDF to do that (I do not know how you get it ? consult you University's purchase/licensing dept. or ICDD marketing people). You can then take representative structure parameters (cell, spacegroup, atomic composition, name, publication data, etc.) from the COD (e.g. from the structure Web page, as mentioned above), and paste those values into the PDF search. The search should yield the structure or structures of the same material, if they exists in the PDF :) > Is there a way that the same COD # could exist for PDF? Since both the COD and the PDF collect published structural data from scientific sources, they should overlap to a large extent (I do not know how much, because I do not have access to the ICSD PDF). Also, if some structure doses not exist in the COD, you can find it in the literature, make a CIF out of it and deposit it to the COD ? the next COD revision will have it, and hopefully in due time Bruker will upgrade Eva to include it :) (but please don't take records from PDF or other non-open database, this violates copyright). However, please keep in mind that the scope of the COD and the PDF databases is slightly different: - the COD collects all *crystal* *structure* data, for both organic and inorganic materials - the PDF started as a collection of powder diffractograms for material identification; thus they have scattering data even in cases when the atomic structure of material is not known, e.g. for clays or amorphous materials. The COD explicitly excludes such data, unless a decent Retveld refinement has been done for the structure. Hope this helps. Sincerely, 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 -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: grazulis.vcf Type: text/x-vcard Size: 4 bytes Desc: not available URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: signature.asc Type: application/pgp-signature Size: 213 bytes Desc: OpenPGP digital signature URL: From rosen at u.northwestern.edu Wed Feb 26 07:00:16 2020 From: rosen at u.northwestern.edu (Andrew Rosen) Date: Tue, 25 Feb 2020 23:00:16 -0600 Subject: [Cod-bugs] Links broken for querying COD Message-ID: Hello, I am trying to query the COD database, but none of the instructions seem to be working. I have tried curl and wget of http://www.crystallography.net/cod/2002926.cif with no luck. I have tried svn co svn://www.crystallography.net/cod and mkdir -p cif; rsync -av --delete rsync://www.crystallography.net/cif/ cif/ and even trying to access http://www.crystallography.net/archives/cod-cifs-mysql.tgz. All these routes give me some flavor of permission issue. Is there a problem with accessing the database right now? Thanks, Andrew -- This message has been scanned for viruses and dangerous content by MailScanner, and is believed to be clean. -------------- next part -------------- An HTML attachment was scrubbed... URL: From grazulis at ibt.lt Wed Feb 26 08:47:49 2020 From: grazulis at ibt.lt (=?UTF-8?Q?Saulius_Gra=c5=beulis?=) Date: Wed, 26 Feb 2020 08:47:49 +0200 Subject: [Cod-bugs] Links broken for querying COD In-Reply-To: References: Message-ID: <3509b6b4-bf2b-35ff-44a8-3a12d1763fa5@ibt.lt> On 2020-02-26 07:00, Andrew Rosen wrote: > I am trying to query the COD database, but none of the instructions > seem to be working. I have tried curl and wget > of?http://www.crystallography.net/cod/2002926.cif with no luck. I have > tried svn co svn://www.crystallography.net/cod > and mkdir -p cif; rsync -av > --delete rsync://www.crystallography.net/cif/ > cif/ and even trying to access > http://www.crystallography.net/archives/cod-cifs-mysql.tgz. All these > routes give me some flavor of permission issue. > > Is there a problem with accessing the database right now? Thank you for your bug report. We are having trouble with the server disk access. I'll investigate and get back to you in a while. Sincerely, -- 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 -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: grazulis.vcf Type: text/x-vcard Size: 4 bytes Desc: not available URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: signature.asc Type: application/pgp-signature Size: 213 bytes Desc: OpenPGP digital signature URL: From grazulis at ibt.lt Wed Feb 26 09:24:11 2020 From: grazulis at ibt.lt (=?UTF-8?Q?Saulius_Gra=c5=beulis?=) Date: Wed, 26 Feb 2020 09:24:11 +0200 Subject: [Cod-bugs] Links broken for querying COD In-Reply-To: References: Message-ID: Dear Andrew, Thank you once more for letting us know about the problems with the COD server. I have rebooted the server, so currently all links and commands that you have specified work; but please see the caveat below: On 2020-02-26 07:00, Andrew Rosen wrote: > I am trying to query the COD database, but none of the instructions > seem to be working. I have tried curl and wget > of?http://www.crystallography.net/cod/2002926.cif with no luck. I have > tried svn co svn://www.crystallography.net/cod > and mkdir -p cif; rsync -av > --delete rsync://www.crystallography.net/cif/ > cif/ and even trying to access > http://www.crystallography.net/archives/cod-cifs-mysql.tgz. All these > routes give me some flavor of permission issue. > The procedure cured the symptom, not the cause, and I am not sure what the cause is. The suspicion is software version incompatibility, so next Monday we have scheduled a software upgrade. This will be announced on the COD we site; there may be short COD service interruptions on that day. Until that, you are welcome to use the COD server but please be prepared that it may halt again unexpectedly (although we'll keep a closer eye on its health ;). I apologise for any inconvenience that this will cause. Sincerely yours, 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 -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: grazulis.vcf Type: text/x-vcard Size: 4 bytes Desc: not available URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: signature.asc Type: application/pgp-signature Size: 213 bytes Desc: OpenPGP digital signature URL: From wanaizuddin at uitm.edu.my Thu Feb 27 12:34:48 2020 From: wanaizuddin at uitm.edu.my (DR. WAN AIZUDDIN W RAZALI) Date: Thu, 27 Feb 2020 18:34:48 +0800 Subject: [Cod-bugs] cod database Message-ID: Hi, Could you please tell me how to download latest COD database? I can't find the link in your website. Thank you Regards Wan -- This message has been scanned for viruses and dangerous content by MailScanner, and is believed to be clean. -------------- next part -------------- An HTML attachment was scrubbed... URL: From sdipietr at fiu.edu Fri Feb 28 05:15:10 2020 From: sdipietr at fiu.edu (Silvina Di Pietro) Date: Fri, 28 Feb 2020 03:15:10 +0000 Subject: [Cod-bugs] COD to PDF Message-ID: Hi Saulius, First of all, I truly appreciate you responding my email and answering my inquiry. You went into great detail. You answered my question when you stated "we are explicitly forbidden to take any data from them, including their identifiers. This restrictiveness is actually one of the main reasons why the COD was started!" I did not mean "Page Description File from Adobe'' but "Powder Diffraction File''. The last two sentences are of great importance as I did not know there was a difference between the two (PDF and COD). I mostly work with clays (illite, muscovite and montmorillonite) so this statement "scattering data even in cases when the atomic structure of material is not known" is good to know since our XRD got the PDF ICDD database as well. I wonder how I am able to know that the atomic structure is not known if the software does the match to my minerals. I'll have to give it a try. Again, I thank you for your time. Have a great day, -Silvi ________________________________ From: Saulius Gra?ulis Sent: Tuesday, February 25, 2020 1:05 AM To: Silvina Di Pietro Cc: cod-bugs at lists.crystallography.net Subject: Re: [Cod-bugs] COD to PDF Dear Silvi, thank you for your message. I'll try to answer your questions below, although I need more context for my answers to be more precise. The short answer would be that we maintain no links with ICDD PDF entries or any other commercial databases. Commercial databases have restrictive licenses, and we are explicitly forbidden to take any data from them, including their identifiers. This restrictiveness is actually one of the main reasons why the COD was started! On 2020-02-18 21:02, Silvina Di Pietro wrote: I had a simple question: I am currently using Eva software on my school's XRD lab. Whenever I match, I get specific COD #. I was wondering if this # could be "translated" into PDF from the ICDD database. What you mean by ?PDF? in this context? Do you mean a Page Description File from Adobe (PDF), generated by ICDD software for a crystallographic entry, or do you mean a record identifier from the powder Diffraction File (PDF) marketed by ICDD? In both cases the answer would be "no", but for different reasons, and thus the workarounds would be different: - if you want a (nice) page description file (PDF) for a structure, then of course we can not run the ICDD software for you on our servers (the software is proprietary), but you can use your browser to find a particular COD structure easily if you know its COD ID ? either use the COD "Search" page and paste the COD ID into the "Search by COD ID:" field, or construct a stable URI for this structure, e.g. for the COD ID 7239975 it would be: https://www.crystallography.net/cod/7239975.html You can then of course use your browser's "print to file" functionality to produce a PDF file. - if you want a corresponding Powder Diffraction File (PDF) identifier, then you have to search for the structure in the PDF using their provided software for the same material. You will have to own a license for PDF to do that (I do not know how you get it ? consult you University's purchase/licensing dept. or ICDD marketing people). You can then take representative structure parameters (cell, spacegroup, atomic composition, name, publication data, etc.) from the COD (e.g. from the structure Web page, as mentioned above), and paste those values into the PDF search. The search should yield the structure or structures of the same material, if they exists in the PDF :) Is there a way that the same COD # could exist for PDF? Since both the COD and the PDF collect published structural data from scientific sources, they should overlap to a large extent (I do not know how much, because I do not have access to the ICSD PDF). Also, if some structure doses not exist in the COD, you can find it in the literature, make a CIF out of it and deposit it to the COD ? the next COD revision will have it, and hopefully in due time Bruker will upgrade Eva to include it :) (but please don't take records from PDF or other non-open database, this violates copyright). However, please keep in mind that the scope of the COD and the PDF databases is slightly different: - the COD collects all crystal structure data, for both organic and inorganic materials - the PDF started as a collection of powder diffractograms for material identification; thus they have scattering data even in cases when the atomic structure of material is not known, e.g. for clays or amorphous materials. The COD explicitly excludes such data, unless a decent Retveld refinement has been done for the structure. Hope this helps. Sincerely, 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 -------------- An HTML attachment was scrubbed... URL: From andrius.merkys at gmail.com Sun Mar 1 08:59:23 2020 From: andrius.merkys at gmail.com (Andrius Merkys) Date: Sun, 1 Mar 2020 08:59:23 +0200 Subject: [Cod-bugs] cod database In-Reply-To: References: Message-ID: <009be17b-99d4-309f-c375-5fa85904af1a@gmail.com> Hi Wan, Various methods to download the contents of the COD are listed here: https://wiki.crystallography.net/howtoobtaincod/ Hope this helps, Andrius On 2020-02-27 12:34, DR. WAN AIZUDDIN W RAZALI wrote: > Hi, > > Could you please tell me how to download latest COD database? > I can't find the link?in your website. > > Thank you > > Regards > Wan > > -- > 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 -- Andrius Merkys 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 Sun Mar 1 09:00:17 2020 From: andrius.merkys at gmail.com (Andrius Merkys) Date: Sun, 1 Mar 2020 09:00:17 +0200 Subject: [Cod-bugs] cod database In-Reply-To: References: Message-ID: <9bb287bc-5117-1b18-1b8f-b211254f6bc8@gmail.com> Hi Wan, Various methods to download the contents of the COD are listed here: https://wiki.crystallography.net/howtoobtaincod/ Hope this helps, Andrius On 2020-02-27 12:34, DR. WAN AIZUDDIN W RAZALI wrote: > Hi, > > Could you please tell me how to download latest COD database? > I can't find the link?in your website. > > Thank you > > Regards > Wan > > -- > 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 -- Andrius Merkys Vilnius University Institute of Biotechnology, Saul?tekio al. 7, room V325 LT-10257 Vilnius, Lithuania -- This message has been scanned for viruses and dangerous content by MailScanner, and is believed to be clean. -------------- next part -------------- An HTML attachment was scrubbed... URL: