From jinbin_hu at 126.com Thu Feb 1 11:21:56 2024 From: jinbin_hu at 126.com (=?GBK?B?uvq99bHzzazRpw==?=) Date: Thu, 1 Feb 2024 17:21:56 +0800 (CST) Subject: [Cod-bugs] A bug about cod-tools Message-ID: <2f9b4383.628a.18d63f98f7c.Coremail.jinbin_hu@126.com> Dear COD-tool development team Developers: hello, I am a graduate student from China, recently in the use of COD - the tools of your development software, I refer to is your link to https://wiki.crystallography.net/cod-tools/#index1h3. In Install the dependencies: Prompt: - Installed: perl-Text-Diff.noarch 0:1.41-5.el7 Dependency Installed: perl-Algorithm-Diff.noarch 0:1.1902-17.el7 Complete! However: In the Build: make - C cod - tools all, does suggest the make - C/home/xonics HuJinbin/cod - the tools/SRC/lib/perl 5 / cod/SPGLib / make[1]: Entering directory `/home/xonics/HuJinbin/cod-tools/src/lib/perl5/COD/SPGLib' make -C .. /.. /.. /.. /externals/spglib make[2]: Entering directory `/home/xonics/HuJinbin/cod-tools/src/externals/spglib' mkdir build mkdir: cannot create directory ?build?: File exists make[2]: *** [build/libsymspg.a] Error 1 make[2]: Leaving directory `/home/xonics/HuJinbin/cod-tools/src/externals/spglib' make[1]: *** [../../../../externals/spglib/build/libsymspg.a] Error 2 make[1]: Leaving directory `/home/xonics/HuJinbin/cod-tools/src/lib/perl5/COD/SPGLib' Make: * * * [/ home/xonics HuJinbin/cod - the tools/SRC/lib/perl 5 / cod/SPGLib PM] Error 2, how should I solve this problem.Looking forward to your reply, thank you Best wishes Jinbin Hu -- 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 Thu Feb 1 11:27:23 2024 From: grazulis at ibt.lt (=?UTF-8?Q?Saulius_Gra=C5=BEulis?=) Date: Thu, 1 Feb 2024 11:27:23 +0200 Subject: [Cod-bugs] A bug about cod-tools In-Reply-To: <2f9b4383.628a.18d63f98f7c.Coremail.jinbin_hu@126.com> References: <2f9b4383.628a.18d63f98f7c.Coremail.jinbin_hu@126.com> Message-ID: <4720501a-cf9e-48c7-90c6-60839442fe7b@ibt.lt> Dear Hu Jinbin, could you please specify exactly which operating system setup (if under a virtual machine (VM): specify if you use Windows Subsytem for Linux WSL, Virtual Box, etc.) and which version of the OS (if under VM ? host and guest OS versions) you use? Sincerely yours, Saulius On 2024-02-01 11:21, ????? wrote: > Dear COD-tool development team > ? ? ? ? ? Developers: hello, I am a graduate student from China, > recently in the use of COD - the tools of your development software, I > refer to is your link to > https://wiki.crystallography.net/cod-tools/#index1h3. In Install the > dependencies: Prompt: - > Installed: > perl-Text-Diff.noarch 0:1.41-5.el7 > Dependency Installed: > perl-Algorithm-Diff.noarch 0:1.1902-17.el7 > Complete! > > However: > In the Build: make - C cod - tools all, does suggest the make - > C/home/xonics HuJinbin/cod - the tools/SRC/lib/perl 5 / cod/SPGLib / > make[1]: Entering directory > `/home/xonics/HuJinbin/cod-tools/src/lib/perl5/COD/SPGLib' > make -C .. /.. /.. /.. /externals/spglib > make[2]: Entering directory > `/home/xonics/HuJinbin/cod-tools/src/externals/spglib' > mkdir build > mkdir: cannot create directory ?build?: File exists > make[2]: *** [build/libsymspg.a] Error 1 > make[2]: Leaving directory > `/home/xonics/HuJinbin/cod-tools/src/externals/spglib' > make[1]: *** [../../../../externals/spglib/build/libsymspg.a] Error 2 > make[1]: Leaving directory > `/home/xonics/HuJinbin/cod-tools/src/lib/perl5/COD/SPGLib' > Make: * * * [/ home/xonics HuJinbin/cod - the tools/SRC/lib/perl 5 / > cod/SPGLib PM] Error 2, > > how should I solve this problem.Looking forward to your reply, thank you > ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ?Best wishes > ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? Jinbin Hu > > -- > 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 -- Dr. Saulius Gra?ulis Vilnius University Institute of Biotechnology, Saul?tekio al. 7 LT-10257 Vilnius, Lietuva (Lithuania) mobile: (+370-684)-49802, (+370-614)-36366 -- 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 Feb 1 11:30:56 2024 From: andrius.merkys at gmail.com (Andrius Merkys) Date: Thu, 1 Feb 2024 11:30:56 +0200 Subject: [Cod-bugs] A bug about cod-tools In-Reply-To: <2f9b4383.628a.18d63f98f7c.Coremail.jinbin_hu@126.com> References: <2f9b4383.628a.18d63f98f7c.Coremail.jinbin_hu@126.com> Message-ID: <32d85f9b-1ae9-4ab0-8988-8f12c0dcc4e8@gmail.com> Hi Jinbin Hu, On 2024-02-01 11:21, ????? wrote: > make[1]: Entering directory > `/home/xonics/HuJinbin/cod-tools/src/lib/perl5/COD/SPGLib' > make -C .. /.. /.. /.. /externals/spglib > make[2]: Entering directory > `/home/xonics/HuJinbin/cod-tools/src/externals/spglib' > mkdir build > mkdir: cannot create directory ?build?: File exists Could you try removing directory 'src/externals/spglib/build/' and building again? This issue sometimes happen when resuming unsuccessful build. A cleaner approach would be to clean the whole cod-tools source (by running 'make distclean') and then running 'make'. Hope this helps, Andrius -- 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 GoldberMG3 at corning.com Thu Feb 1 15:14:07 2024 From: GoldberMG3 at corning.com (Goldberg, Matt (Matthew G)) Date: Thu, 1 Feb 2024 13:14:07 +0000 Subject: [Cod-bugs] Querying for presence of diffraction data Message-ID: Hello- I'm not sure if this is the correct email address to send this question to, but I'm wondering if there's a way to determine whether or not there is diffraction data for a given ID. I know you can go to, e.g., https://www.crystallography.net/cod/2002926.hkl to get the diffraction data if it exists, but I'm wondering if there's a better way than trying to obtain the diffraction data and checking if a 404 error is returned. Nothing is jumping out at me in the REST API documentation to suggest there would be a way to do it through there. Is there some way to do this? If I were to use the SQL option, would there be an easy way to do it that way? Thanks, Matt Goldberg -- 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 Feb 1 15:25:03 2024 From: andrius.merkys at gmail.com (Andrius Merkys) Date: Thu, 1 Feb 2024 15:25:03 +0200 Subject: [Cod-bugs] Querying for presence of diffraction data In-Reply-To: References: Message-ID: <0010a169-ae32-4655-b2c0-849842e3db76@gmail.com> Hi Matt Goldberg, On 2024-02-01 15:14, Goldberg, Matt (Matthew G) wrote: > I?m not sure if this is the correct email address to send this question > to, but I?m wondering if there?s a way to determine whether or not there > is diffraction data for a given ID. I know you can go to, e.g., > https://www.crystallography.net/cod/2002926.hkl to get the diffraction > data if it exists, but I?m wondering if there?s a better way than trying > to obtain the diffraction data and checking if a 404 error is returned. > Nothing is jumping out at me in the REST API documentation to suggest > there would be a way to do it through there. In COD REST API there is a query parameter, 'has_fobs', which when set to 1 will return only those COD entries that have diffraction data files (HKLs) attached. > Is there some way to do this? If I were to use the SQL option, would > there be an easy way to do it that way? You may check if 'flags' SQL column contains 'has_Fobs', viz.: select count(*) from data where flags like "%has_Fobs%" Hope this helps, Andrius -- 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 grazulis at ibt.lt Thu Feb 1 15:26:25 2024 From: grazulis at ibt.lt (=?UTF-8?Q?Saulius_Gra=C5=BEulis?=) Date: Thu, 1 Feb 2024 15:26:25 +0200 Subject: [Cod-bugs] Querying for presence of diffraction data In-Reply-To: References: Message-ID: To second the Andrius' answer: On 2024-02-01 15:14, Goldberg, Matt (Matthew G) wrote: > > I?m not sure if this is the correct email address to send this > question to, but I?m wondering if there?s a way to determine whether > or not there is diffraction data for a given ID. I know you can go to, > e.g., https://www.crystallography.net/cod/2002926.hkl to get the > diffraction data if it exists, but I?m wondering if there?s a better > way than trying to obtain the diffraction data and checking if a 404 > error is returned. Nothing is jumping out at me in the REST API > documentation to suggest there would be a way to do it through there. > > Is there some way to do this? If I were to use the SQL option, would > there be an easy way to do it that way? > If you are happy to use SQL (MySQl or MariaDB), then the following query should answer your question: > mysql -u cod_reader -h sql.crystallography.net cod -e 'select file > from data where flags like "%has fobs%"' Not that there are also many coordinate CIFs that have SHELX HKL file embedded in them; these do not yet show up in the query just mentioned, but we working on it :) HTH, Saulius -- Dr. Saulius Gra?ulis Vilnius University Institute of Biotechnology, Saul?tekio al. 7 LT-10257 Vilnius, Lietuva (Lithuania) mobile: (+370-684)-49802, (+370-614)-36366 -- 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: