From andrius.merkys at gmail.com Mon Apr 19 11:57:34 2021 From: andrius.merkys at gmail.com (Andrius Merkys) Date: Mon, 19 Apr 2021 11:57:34 +0300 Subject: [Cod-bugs] (no subject) In-Reply-To: References: Message-ID: <6d7796b3-1d30-76bd-29c8-a4e5ea870529@gmail.com> Hello, These directories are exposed for public access on purpose. Best wishes, Andrius Merkys On 2021-04-17 09:10, vigneshwaran P wrote: > hi sir,madam > i found a sensible data/directory disclosure on your site. > please verify it . > I'm attaching proof with this mail. > > > thanks. -- This message has been scanned for viruses and dangerous content by MailScanner, and is believed to be clean. From andrius.merkys at gmail.com Tue Apr 20 18:02:01 2021 From: andrius.merkys at gmail.com (Andrius Merkys) Date: Tue, 20 Apr 2021 18:02:01 +0300 Subject: [Cod-bugs] Extracting hkl from cif In-Reply-To: <7734EA68-C7CB-4CE0-83F2-76B1824F786B@gmx.de> References: <01267C34-05FB-4844-B779-E2EBA10CE985@gmx.de> <112e5b47-c919-9a7d-b7bd-fe7b2fc8e990@gmail.com> <7734EA68-C7CB-4CE0-83F2-76B1824F786B@gmx.de> Message-ID: <92fb47f9-d3b3-08ad-fb66-7aea763714a9@gmail.com> Hi Daniel, (Adding Saulius Gra?ulis, the head developer of the COD, to the CC) On 2021-04-16 20:26, Daniel Kratzert wrote: > Here is also another idea. I am thinking for some time now that there should be an option in FinalCif to submit CIF files directly to the COD without using the web site. > What do you think? Is there a REST interface to do so? And how about the checking prior to submission? I think this would be beneficial both for FinalCif users and for the COD. There is a REST interface for deposition, I will send you its description shortly. As for the checks, all data is checked during the deposition, and if any problems occur, the deposition interface responds with issue list. However, client-side checks are also encouraged in order not to overload the server. We have our own set of tools, cod-tools [1], which we use also in the deposition interface. Running cif_cod_check from cod-tools on CIF files prior to the deposition would significantly reduce the load of the COD server. > If you like to do something in FinalCif yourself I would also be happy about pull requests. Great - I will open them on FinalCif GitHub repo. [1] https://wiki.crystallography.net/cod-tools/ Best wishes, Andrius -- Dr. Andrius Merkys Vilnius University Institute of Biotechnology, Saul?tekio al. 7 LT-10257 Vilnius, Lithuania -------------- next part -------------- A non-text attachment was scrubbed... Name: OpenPGP_signature Type: application/pgp-signature Size: 840 bytes Desc: OpenPGP digital signature URL: From matmihalik at saske.sk Wed Apr 21 10:27:07 2021 From: matmihalik at saske.sk (matmihalik at saske.sk) Date: Wed, 21 Apr 2021 09:27:07 +0200 Subject: [Cod-bugs] problems with creating of account Message-ID: <20210421092707.Horde.WBK_wExFy1gYp2W1NxBxMIY@home.saske.sk> Dear COD maintanance I wanted to create an account and to upload some data. I went through the create account page. Then I wanted to log in. I got "incorrect login/password" answer. Well, this was not possible, since I have done copy/paste from the password manager. Nevertheless, I went through "forgot password" option. The page stated: "no username/e-mail match". So I went again through create account page. Here I got message that my e-mail and username is already registered and I should use it!! How was this possible, since few seconds ago I got "no username/e-mail match"? But OK, I have tried to create an account with different username/e-mail. And... the behavior of the web interface was again the same. What is going on? How can I create an account/log in/deposit the data? Best regards Matus Mihalik -- This message has been scanned for viruses and dangerous content by MailScanner, and is believed to be clean. From andrius.merkys at gmail.com Wed Apr 21 10:30:18 2021 From: andrius.merkys at gmail.com (Andrius Merkys) Date: Wed, 21 Apr 2021 10:30:18 +0300 Subject: [Cod-bugs] Extracting hkl from cif In-Reply-To: References: <01267C34-05FB-4844-B779-E2EBA10CE985@gmx.de> <112e5b47-c919-9a7d-b7bd-fe7b2fc8e990@gmail.com> <7734EA68-C7CB-4CE0-83F2-76B1824F786B@gmx.de> Message-ID: <84851f35-e1b2-59b1-c91d-cd2b2d90a6c1@gmail.com> Hi Thomas, On 2021-04-16 22:07, Thomas Munro wrote: > That sounds like a great idea. Anything that makes it simpler to > upload would help get the total up. It might also be good to add that > to StructureFinder, so people with a large collection of old > structures could find and upload them easily. This would indeed be great to have. > A colleague of mine, Doug Ho, has retired and is writing up some old > unpublished structures. He still has all the raw data saved, back to > at least 2008. There must be many people with similar collections, and > it would be great if there was a painless way to deposit them in bulk. > The word could perhaps be put out through IUCR? These unpublished structures would be a great addition to the COD. As for bulk deposition, the COD validation and deposition interface [1] already accepts uploads of archives with many CIF files, thus this could speed up the process. Nevertheless, having "Deposit to COD" button in FinalCif would be surely beneficial. [1] http://www.crystallography.net/cod/deposit Best wishes, Andrius -- Dr. Andrius Merkys Vilnius University Institute of Biotechnology, Saul?tekio al. 7 LT-10257 Vilnius, Lithuania -- This message has been scanned for viruses and dangerous content by MailScanner, and is believed to be clean. From andrius.merkys at gmail.com Wed Apr 21 13:11:57 2021 From: andrius.merkys at gmail.com (Andrius Merkys) Date: Wed, 21 Apr 2021 13:11:57 +0300 Subject: [Cod-bugs] problems with creating of account In-Reply-To: <20210421092707.Horde.WBK_wExFy1gYp2W1NxBxMIY@home.saske.sk> References: <20210421092707.Horde.WBK_wExFy1gYp2W1NxBxMIY@home.saske.sk> Message-ID: <0f9b9bfd-977b-724a-bd41-21d9e510f8ac@gmail.com> Dear Mat?? Mihalik, In the user database I can see two accounts registered to your name today: +--------------+---------------------+-----------------+ | username | email | realname | +--------------+---------------------+-----------------+ | mihalik80 | matmihalik at saske.sk | Mat?? Mihalik | | matusmihalik | mihalik80 at gmail.com | Mat?? Mihalik | +--------------+---------------------+-----------------+ Could you please confirm these are the accounts that you are talking about? Please note that after registration you have to confirm your e-mail address by clicking a link in an e-mail sent to you automatically. Only after that you will be allowed to log in. Also please note that to login you need to enter your username, not e-mail address. Also in the user database I see that you have successfully requested for password reset for username 'mihalik80'. Have you received an e-mail with a link to do so? Did you try resetting your password with that link? Best wishes, Andrius Merkys On 2021-04-21 10:27, matmihalik at saske.sk wrote: > Dear COD maintanance > > I wanted to create an account and to upload some data. I went through > the create account > page. Then I wanted to log in. I got "incorrect login/password" answer. > Well, this was not possible, since I have done copy/paste from the > password manager. Nevertheless, I went through "forgot password" option. > The page stated: "no username/e-mail match". So I went again through > create account page. Here I got message that my e-mail and username is > already registered and I should use it!! How was this possible, since > few seconds ago I got "no username/e-mail match"? But OK, I have tried > to create an account with different username/e-mail. And... the behavior > of the web interface was again the same. > > What is going on? How can I create an account/log in/deposit the data? > > Best regards > Matus Mihalik -- Dr. Andrius Merkys Vilnius University Institute of Biotechnology, Saul?tekio al. 7 LT-10257 Vilnius, Lithuania -- This message has been scanned for viruses and dangerous content by MailScanner, and is believed to be clean. From andrius.merkys at gmail.com Wed Apr 21 13:14:50 2021 From: andrius.merkys at gmail.com (Andrius Merkys) Date: Wed, 21 Apr 2021 13:14:50 +0300 Subject: [Cod-bugs] Extracting hkl from cif In-Reply-To: <7734EA68-C7CB-4CE0-83F2-76B1824F786B@gmx.de> References: <01267C34-05FB-4844-B779-E2EBA10CE985@gmx.de> <112e5b47-c919-9a7d-b7bd-fe7b2fc8e990@gmail.com> <7734EA68-C7CB-4CE0-83F2-76B1824F786B@gmx.de> Message-ID: <90ad39a5-8291-5b04-ee20-c7f867b72873@gmail.com> Hi Daniel, On 2021-04-16 20:26, Daniel Kratzert wrote: > Here is also another idea. I am thinking for some time now that there should be an option in FinalCif to submit CIF files directly to the COD without using the web site. > What do you think? Is there a REST interface to do so? And how about the checking prior to submission? I have described the COD deposition API here: https://wiki.crystallography.net/RESTful_API/#index3h1 Please let me know should you need any further information. Best wishes, Andrius -- Dr. Andrius Merkys Vilnius University Institute of Biotechnology, Saul?tekio al. 7 LT-10257 Vilnius, Lithuania -- This message has been scanned for viruses and dangerous content by MailScanner, and is believed to be clean. From andrius.merkys at gmail.com Wed Apr 21 14:57:00 2021 From: andrius.merkys at gmail.com (Andrius Merkys) Date: Wed, 21 Apr 2021 14:57:00 +0300 Subject: [Cod-bugs] problems with creating of account In-Reply-To: <20210421123725.Horde.D03FyHXdL8dy3fSw0i9L19U@home.saske.sk> References: <20210421092707.Horde.WBK_wExFy1gYp2W1NxBxMIY@home.saske.sk> <0f9b9bfd-977b-724a-bd41-21d9e510f8ac@gmail.com> <20210421123725.Horde.D03FyHXdL8dy3fSw0i9L19U@home.saske.sk> Message-ID: <083359d2-93e4-5c44-df3e-49e8be77ef00@gmail.com> Dear Mat?? Mihalik, I am glad to hear that you have sorted this issue out. I will look into making the notice about activation e-mail more visible. Many thanks for your contribution to the COD! Best wishes, Andrius Merkys On 2021-04-21 13:37, matmihalik at saske.sk wrote: > Dear Andrius Merkys > > after I have sent you an e-mail, I have noticed the e-mails in my inbox. > I did not noticed on the web site that I will get the activation e-mail > and I have to activate the account. So, problem is solved, both accounts > work and I have already deposited the data. > > BEst regards > Matus Mihalik -- Dr. Andrius Merkys Vilnius University Institute of Biotechnology, Saul?tekio al. 7 LT-10257 Vilnius, Lithuania -- This message has been scanned for viruses and dangerous content by MailScanner, and is believed to be clean. From alex.dytso at njit.edu Thu Apr 22 17:27:08 2021 From: alex.dytso at njit.edu (Dytso, Alex) Date: Thu, 22 Apr 2021 10:27:08 -0400 Subject: [Cod-bugs] Raman Database Message-ID: To Whom It May Concern, I am writing to you with regards to the Raman database that we have found at: https://solsa.crystallography.net/rod/index.php We were wondering if this database is accessible via a single file and whether you can share this file with us. We are currently pursuing a machine learning project and your dataset looks like what we need for this project. We would greatly appreciate any assistance with this that you can provide. Thank you! Best, Alex [image: NJIT logo] *Alex Dytso* Assistant Professor Electrical and Computer Engineering alex.dytso at njit.edu ? (973) 596-5710 <9735965710> -- 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 andrius.merkys at gmail.com Thu Apr 22 19:13:37 2021 From: andrius.merkys at gmail.com (Andrius Merkys) Date: Thu, 22 Apr 2021 19:13:37 +0300 Subject: [Cod-bugs] Raman Database In-Reply-To: References: Message-ID: <832e56c1-e9d9-dc43-04d2-ea6364262bfb@gmail.com> Dear Alex Dytso, I assume you wish to download all the contents of the ROD at once. This could be achieved by submitting an empty query in the search page, leading to [1]. On search result page you may click "archive of ROD files (ZIP)" to download all ROD files in a single ZIP archive. Let me know whether this is what you need. [1] https://solsa.crystallography.net/rod/result.php Best wishes, Andrius Merkys On 2021-04-22 17:27, Dytso, Alex wrote: > To Whom It May Concern,?? > I am writing to you with regards to the Raman database that we have > found at: https://solsa.crystallography.net/rod/index.php > > > We were wondering if this database is accessible?via a single file and > whether you can share this file with us.? We are currently pursuing?a > machine learning project and your dataset looks like what we need for > this project.?? > > We would greatly appreciate any assistance with this that you can provide.? > Thank you!? > > Best, > Alex? > > NJIT logo *Alex Dytso* > Assistant Professor > Electrical and Computer Engineering > alex.dytso at njit.edu ???(973)?596-5710 > -- Dr. Andrius Merkys Vilnius University Institute of Biotechnology, Saul?tekio al. 7 LT-10257 Vilnius, Lithuania -- This message has been scanned for viruses and dangerous content by MailScanner, and is believed to be clean. From nbehrnd at yahoo.com Fri Apr 23 20:21:12 2021 From: nbehrnd at yahoo.com (Norwid Behrnd) Date: Fri, 23 Apr 2021 17:21:12 +0000 Subject: [Cod-bugs] possible doublette entry / suggest of consolidation #9013110 and #9016483 References: <20210423172112.4f5fc7fa.ref@carnot2> Message-ID: <20210423172112.4f5fc7fa@carnot2> Dear maintainers of the COD, I would like to suggest two data sets in the COD to be merged into one for that they describe the same crystallographic model. Some moments ago I noticed a question on chemistry.stackechange.com about phosphorous.[1] On occasion, arguments for one or the other point of view, and equally questions consider crystallography (including reference to the COD), too. Curious about relevant data in the COD accessed on-line, I noticed entries #9013110 and #9016483 practically describe the same model: It is not only by the authors and publication, or about the same space group, but same about the experimental temperature .and. lattice constants .and. atomic coordinates. Based on these observations and assuming this might be supported on your database policy, I would like to suggest that either one of the two entries seen today (2021-04-23) coalesces into the other, e.g. the ChemSpider based #9013110 into the AMCSD based #9016483, then with a reference to ChemSpider. The attachment of this e-mail documents my findings. With best regards, Norwid Behrnd ---- 8>< ---- md5sum ---- ---- attached files ---- 8f4a56561d03f7063a4b8cf251b189d7 9013110.cif 046b9ea09245ebda526345630660afcc 9016483.cif 011e69b7e310a3618b13fdf1cfa9386a vimdiff_01.png 62ccac3de6ade94c79cc5dc0b6dd43b4 vimdiff_02.png ---- 8>< ---- [1] https://chemistry.stackexchange.com/questions/150430/difference-between-white-and-yellow-phosphorus -- This message has been scanned for viruses and dangerous content by MailScanner, and is believed to be clean. -------------- next part -------------- A non-text attachment was scrubbed... Name: vimdiff_02.png Type: image/png Size: 105775 bytes Desc: not available URL: -------------- next part -------------- A non-text attachment was scrubbed... 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<2b2b8b13-929c-f5f6-d3cd-107e0f72ce5c@ibt.lt> Dear Norwid, thank you very much for the report! On 2021-04-23 20:21, Norwid Behrnd wrote: > I would like to suggest two data sets in the COD to be merged into > one for that they describe the same crystallographic model. > > Some moments ago I noticed a question on chemistry.stackechange.com > about phosphorous.[1] On occasion, arguments for one or the other > point of view, and equally questions consider crystallography > (including reference to the COD), too. > > Curious about relevant data in the COD accessed on-line, I noticed > entries #9013110 and #9016483 practically describe the same model: > It is not only by the authors and publication, or about the same > space group, but same about the experimental temperature .and. lattice > constants .and. atomic coordinates. > Indeed, the two structures you mention seem to be the same. The COD policy in that case would to mark one entry as a duplicate of the other one (of the more complete one). We'll check the original paper and mark the entries accordingly. Unfortunately, duplicates occasionally end up in the COD; when detected, they are marked in the 'duplicateof' column in the COD SQL table `data`, and using the '_cod_duplicate_entry' CIF data name in the duplicate entry CIF.? When doing statistics on the COD, these need to be excluded (our search we page also does this). We do not delete these entries so that the COD IDs, once assigned, always point to the record of the same crystal investigation. Sincerely yours, Saulius -- Dr. Saulius Gra?ulis Vilnius University, Life Science Center, Institute of Biotechnology Saul?tekio al. 7, LT-10257 Vilnius, Lietuva (Lithuania) phone (office): (+370-5)-2234353, mobile: (+370-684)-49802, (+370-614)-36366 -------------- 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... 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