From aconstantinides1 at student.gsu.edu Mon Oct 2 20:30:50 2017 From: aconstantinides1 at student.gsu.edu (Amanda Constantinides) Date: Mon, 2 Oct 2017 17:30:50 +0000 Subject: [Cod-bugs] "No data blocks that contain coordinates found" Message-ID: Hi, I am trying to deposit several structures in the COD in preparation for publication in Crystals. I used PDB_extract to convert structure factor and coordinate files to .CIF format. When I tried to upload either of these compressed CIF files, the error message "no data blocks that contain coordinates found" came up. When I tried to add diffraction data files (.mtz files with .lp files converted to .cif files in PDB_extract), new error messages came up. How can I deposit these structures? Thank you, Amanda Constantinides Graduate Research Assistant Georgia State University -------------- next part -------------- An HTML attachment was scrubbed... URL: From antanas.vaitkus90 at gmail.com Mon Oct 2 22:12:36 2017 From: antanas.vaitkus90 at gmail.com (Antanas Vaitkus) Date: Mon, 2 Oct 2017 22:12:36 +0300 Subject: [Cod-bugs] "No data blocks that contain coordinates found" In-Reply-To: References: Message-ID: Dear Amanda Constantinides, thank you for taking interest in the COD. Could you please send an example of the CIF files you are trying to upload so we could investigate further? Sincerely, Antanas Vaitkus 2017-10-02 20:30 GMT+03:00 Amanda Constantinides < aconstantinides1 at student.gsu.edu>: > Hi, > > I am trying to deposit several structures in the COD in preparation for > publication in *Crystals*. I used PDB_extract to convert structure factor > and coordinate files to .CIF format. When I tried to upload either of these > compressed CIF files, the error message "no data blocks that contain > coordinates found" came up. When I tried to add diffraction data files > (.mtz files with .lp files converted to .cif files in PDB_extract), new > error messages came up. > > How can I deposit these structures? > > Thank you, > > Amanda Constantinides > Graduate Research Assistant > Georgia State University > > > > _______________________________________________ > 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 Tue Oct 3 16:30:11 2017 From: antanas.vaitkus90 at gmail.com (Antanas Vaitkus) Date: Tue, 3 Oct 2017 16:30:11 +0300 Subject: [Cod-bugs] "No data blocks that contain coordinates found" In-Reply-To: References: Message-ID: Dear Amanda, am I correct to assume that You are trying to deposit a protein crystal structure? The scope of the COD does not include biopolymers since this domain is already well covered by the PDB database. Is there any reason not to deposit your crystal structure to the PDB database? Sincerely, Antanas Vaitkus 2017-10-03 14:13 GMT+03:00 Amanda Constantinides < aconstantinides1 at student.gsu.edu>: > Hi Antanas, > I can not send any data. It is not published yet. I have a regular PDB > file, an .mtz file, a log file (.lp), and a .sca file. What is the best way > to convert them to .cif format to be uploaded into the COD? My attempt > using PDB_extract was not successful. > > Thank you, > > Amanda Constantinides > ------------------------------ > *From:* Antanas Vaitkus > *Sent:* Monday, October 2, 2017 3:12:36 PM > *To:* Amanda Constantinides > *Cc:* cod-bugs at ibt.lt > *Subject:* Re: [Cod-bugs] "No data blocks that contain coordinates found" > > Dear Amanda Constantinides, > > thank you for taking interest in the COD. Could you please send an example > of the CIF files you are trying to upload so we could investigate further? > > Sincerely, > Antanas Vaitkus > > 2017-10-02 20:30 GMT+03:00 Amanda Constantinides < > aconstantinides1 at student.gsu.edu>: > >> Hi, >> >> I am trying to deposit several structures in the COD in preparation for >> publication in *Crystals*. I used PDB_extract to convert structure >> factor and coordinate files to .CIF format. When I tried to upload either >> of these compressed CIF files, the error message "no data blocks that >> contain coordinates found" came up. When I tried to add diffraction data >> files (.mtz files with .lp files converted to .cif files in PDB_extract), >> new error messages came up. >> >> How can I deposit these structures? >> >> Thank you, >> >> Amanda Constantinides >> Graduate Research Assistant >> Georgia State University >> >> >> >> _______________________________________________ >> 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 > > > -- 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 Oct 4 09:40:54 2017 From: antanas.vaitkus90 at gmail.com (Antanas Vaitkus) Date: Wed, 4 Oct 2017 09:40:54 +0300 Subject: [Cod-bugs] "No data blocks that contain coordinates found" In-Reply-To: References: Message-ID: Dear Amanda, the requirements are indeed a bit misleading -- neither of the repositories recommended by the "Crystals" journal (COD, CSD) accept crystal structures of proteins. I would assume that the PDB was accidentally omitted in the recommendations on the basis that depositing protein structures to the PDB prior to publication has become a *de facto* standard nowadays. I will write an e-mail to the "Crystals" editorial board asking them to update the instructions. As for now, I would assume that the best solution for you would be to deposit your data to the PDB and simply reference it in the paper. Sincerely, Antanas Vaitkus 2017-10-03 18:29 GMT+03:00 Amanda Constantinides < aconstantinides1 at student.gsu.edu>: > This is what is on the website:http://www.mdpi.com/ > journal/crystals/instructions > > *"X-Ray Crystallographic Data:**Crystals**deposit the crystallographic > data prior to the submission of the manuscript* > > - *COD:* Preferably, the data should be deposited with the Crystallography > Open Database (COD) . Please deposit > as "pre-publication data" at http://www.crystallography. > net/initiate_deposition.php prior to the submission of the manuscript. > COD numbers for structures will be displayed immediately after the data is > validated and deposited, and should be included in the manuscript, along > with the following text: "COD ...... contains the supplementary > crystallographic data for this paper. These data can be obtained free of > charge via http://www.crystallography.net/search.html". This text may > be included in the experimental section or as a suitably referenced > endnote." > > I am not sure how I have misinterpreted this. > > Best, > > Amanda Constantinides > > > Crystals | Instructions for Authors > > www.mdpi.com > Crystals, an international, peer-reviewed Open Access journal. > > > > ------------------------------ > *From:* Amanda Constantinides > *Sent:* Tuesday, October 3, 2017 11:26:38 AM > *To:* Antanas Vaitkus > > *Subject:* Re: [Cod-bugs] "No data blocks that contain coordinates found" > > > Hi Antanas, > Ohhhh ok!!! I must have misread the directions for submission in the > journal *Crystals*. I was also wondering why the PDB was not sufficient > for this journal. I will check the directions again. > > > Thank you! > > Amanda Constantinides > ------------------------------ > *From:* Antanas Vaitkus > *Sent:* Tuesday, October 3, 2017 9:30:11 AM > *To:* Amanda Constantinides; cod-bugs at ibt.lt > *Subject:* Re: [Cod-bugs] "No data blocks that contain coordinates found" > > Dear Amanda, > > am I correct to assume that You are trying to deposit a protein crystal > structure? The scope of the COD does not include biopolymers since this > domain is already well covered by the PDB database. > > Is there any reason not to deposit your crystal structure to the PDB > database? > > Sincerely, > Antanas Vaitkus > > 2017-10-03 14:13 GMT+03:00 Amanda Constantinides < > aconstantinides1 at student.gsu.edu>: > >> Hi Antanas, >> I can not send any data. It is not published yet. I have a regular PDB >> file, an .mtz file, a log file (.lp), and a .sca file. What is the best way >> to convert them to .cif format to be uploaded into the COD? My attempt >> using PDB_extract was not successful. >> >> Thank you, >> >> Amanda Constantinides >> ------------------------------ >> *From:* Antanas Vaitkus >> *Sent:* Monday, October 2, 2017 3:12:36 PM >> *To:* Amanda Constantinides >> *Cc:* cod-bugs at ibt.lt >> *Subject:* Re: [Cod-bugs] "No data blocks that contain coordinates found" >> >> Dear Amanda Constantinides, >> >> thank you for taking interest in the COD. Could you please send an >> example of the CIF files you are trying to upload so we could investigate >> further? >> >> Sincerely, >> Antanas Vaitkus >> >> 2017-10-02 20:30 GMT+03:00 Amanda Constantinides < >> aconstantinides1 at student.gsu.edu>: >> >>> Hi, >>> >>> I am trying to deposit several structures in the COD in preparation for >>> publication in *Crystals*. I used PDB_extract to convert structure >>> factor and coordinate files to .CIF format. When I tried to upload either >>> of these compressed CIF files, the error message "no data blocks that >>> contain coordinates found" came up. When I tried to add diffraction data >>> files (.mtz files with .lp files converted to .cif files in PDB_extract), >>> new error messages came up. >>> >>> How can I deposit these structures? >>> >>> Thank you, >>> >>> Amanda Constantinides >>> Graduate Research Assistant >>> Georgia State University >>> >>> >>> >>> _______________________________________________ >>> 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 >> >> >> > > > -- > Antanas Vaitkus, > PhD student at Vilnius University Institute of Biotechnology, > room V325, Saul?tekio al. 7 > , > LT-10257 Vilnius, Lithuania > > > -- 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 Oct 4 10:10:54 2017 From: antanas.vaitkus90 at gmail.com (Antanas Vaitkus) Date: Wed, 4 Oct 2017 10:10:54 +0300 Subject: [Cod-bugs] Clarification of instructions for authors Message-ID: Dear Sir/Madam, I am writing on behalf of the Crystallography Open Database (COD) which is one of the repositories for X-Ray Crystallographic Data recommended by your journal. Recently, an attempt was made to deposit a protein crystal structure to our database; after a short exchange with the author it was made clear that she was simply following the instructions provided on your website (http://www.mdpi.com/journal/crystals/instructions). Protein crystal structures are out of the scope of the COD (as well as your other recommended repository -- the Cambridge Crystallographic Data Centre (CCDC)) since the field is well covered by the Protein Data Bank (PDB). Would it be possible to update your instructions to reflect that the protein structures should indeed be deposited to the PDB? Sincerely, Antanas Vaitkus -- 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 helmut.coelfen at uni-konstanz.de Wed Oct 4 10:41:03 2017 From: helmut.coelfen at uni-konstanz.de (Helmut =?UTF-8?B?Q8O2bGZlbg==?=) Date: Wed, 04 Oct 2017 09:41:03 +0200 Subject: [Cod-bugs] Clarification of instructions for authors In-Reply-To: References: Message-ID: Dear Mr. Vaitkus, many thanks for pointing this out to us so that the info on the swebsite can be updated accordingly. Best wishes Helmut C?lfen __________________________________________________________________ Prof. Dr. Helmut C?lfen, FRSC University of Konstanz Physical Chemistry Universit?tsstra?e 10, Box 714 D-78457 Konstanz Tel +49 (0) 7531 88-4063 (Office) +49 (0) 7531 88-2027 (Secretary Ms. K?st) Fax +49 (0) 7531 88-3139 https://www.chemie.uni-konstanz.de/coelfen/ __________________________________________________________________ Von: Antanas Vaitkus Datum: Mittwoch, 4. Oktober 2017 um 09:10 An: Cc: Helmut C?lfen , Amanda Constantinides , Betreff: Clarification of instructions for authors Dear Sir/Madam, I am writing on behalf of the Crystallography Open Database (COD) which is one of the repositories for X-Ray Crystallographic Data recommended by your journal. Recently, an attempt was made to deposit a protein crystal structure to our database; after a short exchange with the author it was made clear that she was simply following the instructions provided on your website (http://www.mdpi.com/journal/crystals/instructions). Protein crystal structures are out of the scope of the COD (as well as your other recommended repository -- the Cambridge Crystallographic Data Centre (CCDC)) since the field is well covered by the Protein Data Bank (PDB). Would it be possible to update your instructions to reflect that the protein structures should indeed be deposited to the PDB? Sincerely, Antanas Vaitkus -- 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: