From jz449 at cam.ac.uk Mon Sep 16 18:04:56 2019 From: jz449 at cam.ac.uk (J. Zhao) Date: Mon, 16 Sep 2019 16:04:56 +0100 Subject: [Cod-bugs] Query about experimental condition information for entries Message-ID: <8c65c8f4dd16a38c50ab4de8b5ef7ad9@cam.ac.uk> Hi, I am wondering is it possible to obtain any information of experimental condition for the entries? I.e. under what experimental condition did the author measure this structure? Or like under what temperature one entry is stable, or whether it is the most stable structure at room temperature? The problem I met is, if I query with 'ZnS', COD returns tens of structures, and I would like to use the one that is most stable under room temperature. So is it possible to perform such selection through COD system or API? Many thanks! Regards, Jiuyang -------------- next part -------------- An HTML attachment was scrubbed... URL: From andrius.merkys at gmail.com Tue Sep 17 10:38:48 2019 From: andrius.merkys at gmail.com (Andrius Merkys) Date: Tue, 17 Sep 2019 10:38:48 +0300 Subject: [Cod-bugs] Query about experimental condition information for entries In-Reply-To: <8c65c8f4dd16a38c50ab4de8b5ef7ad9@cam.ac.uk> References: <8c65c8f4dd16a38c50ab4de8b5ef7ad9@cam.ac.uk> Message-ID: <53b74e71-2694-2d3f-1e18-bd878f5506ee@gmail.com> Hi Jiuyang, On 2019-09-16 18:04, J. Zhao wrote: > > I am wondering is it possible to obtain any information of > experimental condition for the entries? I.e. under what experimental > condition did the author measure this structure? > Yes, this information is present in CIF files of individual entries, under CIF data items '_diffrn_ambient_pressure' [1] and '_diffrn_ambient_temperature' [2]. You may either examine individual CIF files for values of these data items, or query the COD MySQL database (see [3] for details) for values of 'diffrtemp' and 'diffrpressure', correspondingly (see [4] for details). > Or like under what temperature one entry is stable, or whether it is > the most stable structure at room temperature? > > The problem I met is, if I query with 'ZnS', COD returns tens of > structures, and I would like to use the one that is most stable under > room temperature. > Currently, the COD does not contain information about the stability of its entries. Hope this helps, Andrius [1] https://www.iucr.org/__data/iucr/cifdic_html/1/cif_core.dic/Idiffrn_ambient_pressure.html [2] https://www.iucr.org/__data/iucr/cifdic_html/1/cif_core.dic/Idiffrn_ambient_temperature.html [3] http://wiki.crystallography.net/howtoquerycod/ [4] http://wiki.crystallography.net/cod_mysql_schema/ -- Andrius Merkys Vilnius University Institute of Biotechnology, Saul?tekio al. 7, room V325 LT-10257 Vilnius, Lithuania From andrius.merkys at gmail.com Wed Sep 18 13:30:16 2019 From: andrius.merkys at gmail.com (Andrius Merkys) Date: Wed, 18 Sep 2019 13:30:16 +0300 Subject: [Cod-bugs] Query about experimental condition information for entries In-Reply-To: <69c43224c3b8ef88a51cafea75629efe@cam.ac.uk> References: <8c65c8f4dd16a38c50ab4de8b5ef7ad9@cam.ac.uk> <53b74e71-2694-2d3f-1e18-bd878f5506ee@gmail.com> <69c43224c3b8ef88a51cafea75629efe@cam.ac.uk> Message-ID: <3d198be3-96ad-19cc-fdbc-1645a2a72466@gmail.com> Dear Jiuyang, On 2019-09-17 15:55, J. Zhao wrote: > > I notice that only very few entires have?'_diffrn_ambient_pressure' > and?'_diffrn_ambient_temperature', only around 1.9k out of ~400,000. > > Is it normal or my problem of searching? > I have checked the counts of entries with defined 'diffrtemp' ('_diffrn_ambient_temperature') and 'diffrpressure' ('_diffrn_ambient_pressure') values: andrius at suopis ~ $ mysql -u cod_reader -h www.crystallography.net cod -e 'select count(*) from data where diffrtemp is not null' -N +--------+ | 344017 | +--------+ andrius at suopis ~ $ mysql -u cod_reader -h www.crystallography.net cod -e 'select count(*) from data where diffrpressure is not null' -N +------+ | 3353 | +------+ So while the number of records with pressure is really low, 3/4 of all the records contain information about temperature. Hope this helps, Andrius -- Andrius Merkys Vilnius University Institute of Biotechnology, Saul?tekio al. 7, room V325 LT-10257 Vilnius, Lithuania From darryl.borland at unibas.ch Fri Sep 20 15:42:49 2019 From: darryl.borland at unibas.ch (Darryl Borland) Date: Fri, 20 Sep 2019 12:42:49 +0000 Subject: [Cod-bugs] COD Message-ID: <6ec074a77884422dae49f8fc5235a9d0@unibas.ch> Good afternoon, I do not have much experience with COD and XRD for that matter, but I am learning. For security reasons in our department at the University we do not have our computer on the network only intranet for data storage etc. Is it possible to have an offline version of the COD? Thanks again and I apologize for the dopey questions. Darryl [https://pharma.unibas.ch/fileadmin/pharma/images/logo-institute.png] Basel University Dept. of Pharmaceutical Technology 50 Klingelbergstrasse CH-4056 Basel +41612071502 -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: image001.png Type: image/png Size: 4340 bytes Desc: image001.png URL: From antanas.vaitkus90 at gmail.com Fri Sep 20 15:59:49 2019 From: antanas.vaitkus90 at gmail.com (Antanas Vaitkus) Date: Fri, 20 Sep 2019 15:59:49 +0300 Subject: [Cod-bugs] COD In-Reply-To: <6ec074a77884422dae49f8fc5235a9d0@unibas.ch> References: <6ec074a77884422dae49f8fc5235a9d0@unibas.ch> Message-ID: Dear Darryl Borland, thank you for your interest in the COD. Yes, an offline version of the COD can be acquired in multiple ways which are described on the following page: http://wiki.crystallography.net/howtoobtaincod/. Please let us if you have any additional questions or if you encounter any problems while retrieving the files. Sincerely, Antanas Vaitkus On Fri, 20 Sep 2019 at 15:44, Darryl Borland wrote: > Good afternoon, > > > > I do not have much experience with COD and XRD for that matter, but I am > learning. For security reasons in our department at the University we do > not have our computer on the network only intranet for data storage etc. > Is it possible to have an offline version of the COD? > > > > Thanks again and I apologize for the dopey questions. > > > > Darryl > > > > > > [image: > https://pharma.unibas.ch/fileadmin/pharma/images/logo-institute.png] > > Basel University > > Dept. of Pharmaceutical Technology > > 50 Klingelbergstrasse > > CH-4056 Basel > > +41612071502 > > > > > > > > > _______________________________________________ > 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: -------------- next part -------------- A non-text attachment was scrubbed... Name: image001.png Type: image/png Size: 4340 bytes Desc: not available URL: From antanas.vaitkus90 at gmail.com Fri Sep 20 20:01:16 2019 From: antanas.vaitkus90 at gmail.com (Antanas Vaitkus) Date: Fri, 20 Sep 2019 20:01:16 +0300 Subject: [Cod-bugs] COD In-Reply-To: <43e75f0804e243bf85f39cffe43d50ed@unibas.ch> References: <6ec074a77884422dae49f8fc5235a9d0@unibas.ch> <43e75f0804e243bf85f39cffe43d50ed@unibas.ch> Message-ID: Dear Daryl, sadly, I do not have any experience with PDXL so I am unsure if raw CIF files can be directly imported to be used for phase identification. However, Rigaku have provided us with a precompiled index file that can be used for this purpose. Instructions on how to install it as well as the index file itself can be acquired here: http://www.crystallography.net/cod/archives/2016/Rigaku. I will send this reply back to the 'cod-bugs' mailing list in case my colleagues have some additional comments. Please inform us of your progress. Sincerely, Antanas Vaitkus On Fri, 20 Sep 2019 at 18:53, Darryl Borland wrote: > Hi Antanas, > > > > We downloaded the following > > > > > > We are using PDXL on our Rigaku XRD. Are there any installation > guidelines? We are trying to import the CIF files this seemed to work but > I think we might be doing something wrong. If you have any info that we > read for next week that would be great. > > > > Have a nice weekend, > > > > Darryl > > > > > > *From:* Antanas Vaitkus [mailto:antanas.vaitkus90 at gmail.com] > *Sent:* Friday, September 20, 2019 3:00 PM > *To:* Darryl Borland > *Cc:* cod-bugs at ibt.lt > *Subject:* Re: [Cod-bugs] COD > > > > Dear Darryl Borland, > > thank you for your interest in the COD. Yes, an offline version of the COD > can be acquired in multiple ways > which are described on the following page: > http://wiki.crystallography.net/howtoobtaincod/. > > Please let us if you have any additional questions or if you encounter any > problems while retrieving the files. > > Sincerely, > > Antanas Vaitkus > > > > On Fri, 20 Sep 2019 at 15:44, Darryl Borland > wrote: > > Good afternoon, > > > > I do not have much experience with COD and XRD for that matter, but I am > learning. For security reasons in our department at the University we do > not have our computer on the network only intranet for data storage etc. > Is it possible to have an offline version of the COD? > > > > Thanks again and I apologize for the dopey questions. > > > > Darryl > > > > > > [image: > https://pharma.unibas.ch/fileadmin/pharma/images/logo-institute.png] > > Basel University > > Dept. of Pharmaceutical Technology > > 50 Klingelbergstrasse > > CH-4056 Basel > > +41612071502 > > > > > > > > > > _______________________________________________ > 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... 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