From tsiegler at utexas.edu Tue Apr 3 16:07:35 2018 From: tsiegler at utexas.edu (Timothy D Siegler) Date: Tue, 3 Apr 2018 15:07:35 +0200 Subject: [Cod-bugs] A certain CIF is crashing the new version of Mercury Message-ID: To whom it may concern: I just downloaded the new version of Mercury. In the new version, CIF #1545320 will not load.I tried using both my old copy and a newly downloaded copy of this CIF file, but both crash my program. Other CIF files I have tried from the database load perfectly well. Thanks! Tim -- *Timothy D Siegler *| NDSEG Fellow, Korgel Group The University of Texas at Austin | McKetta Department of Chemical Engineering | Cockrell School of Engineering 100 E. 24th St. Austin, TX 78712 | NHB 6.352 | 512-471-7043 | tsiegler at utexas.edu -------------- next part -------------- An HTML attachment was scrubbed... URL: From grazulis at ibt.lt Tue Apr 3 16:30:07 2018 From: grazulis at ibt.lt (=?UTF-8?Q?Saulius_Gra=c5=beulis?=) Date: Tue, 3 Apr 2018 16:30:07 +0300 Subject: [Cod-bugs] A certain CIF is crashing the new version of Mercury In-Reply-To: References: Message-ID: Hi, On 2018-04-03 16:07, Timothy D Siegler wrote: > I just downloaded the new version of Mercury. In the new version, CIF > #1545320 will not load.I tried using both my old copy and a newly > downloaded copy of this CIF file, but both crash my program.? > > Other CIF files I have tried from the database load perfectly well.? Since you have just downloaded the new Mercury, it seems like the most probable reason is in the Mercury itself ? you may want to submit a bug report to CCDC. I've just looked at the current COD 1545320 entry, it looks fairly OK: the syntax is correct (checked with cod-tools cifparse, vcif, pycifrw), validator has only minor complaints (_space_group_symop_id is missing, usually not a problem for most programs), Jmol, Rasmol and Pymol on Ubuntu 16.04 read and display the file just fine, and cif_molecule processes it OK. The calculated cell contents matches the declared one. The problem might be a large _shelx_res_file data item (you may want to remove it from the file and try Mercury again), but it is smaller than many other instances of this data item ? it would be strange if it causes problems... You can also try the previous revision of this file from http://www.crystallography.net/cod/1545320.cif at 194862 , but the differences are minor indeed, just bibliography info was added. Other than that I have really no ideas why Mercury crashes. Unless CCDC publish Mercury source code under a F/LOSS license and I can run the code under debugger, we have virtually no means to tell what is going inside the program. Regards, 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 From andrius.merkys at gmail.com Tue Apr 3 16:33:48 2018 From: andrius.merkys at gmail.com (Andrius Merkys) Date: Tue, 3 Apr 2018 16:33:48 +0300 Subject: [Cod-bugs] A certain CIF is crashing the new version of Mercury In-Reply-To: References: Message-ID: Dear Timothy, the CIF of COD entry 1545320 is syntactically correct according to the CIF 1.1 syntax. As Mercury is a closed-source program, I can not investigate the exact cause of the problem with it. Nevertheless, I have checked the CIF with cif_linguist (https://github.com/COMCIFS/cif_api), CIF developer's implementation of the CIF parser, to find out that cif_linguist requires CIF value 'Fc^*^=kFc[1+0.001xFc^2^\l^3^/sin(2\q)]^-1/4^' be quoted (I have submitted a bug report, https://github.com/COMCIFS/cif_api/issues/22). The same reason may be with Mercury. You may try to remove the CIF line with _refine_ls_extinction_expression data item and try again to test it. Best wishes, Andrius On 04/03/2018 04:07 PM, Timothy D Siegler wrote: > To whom it may concern: > > I just downloaded the new version of Mercury. In the new version, CIF #1545320 will not load.I tried using both my old copy and a newly downloaded copy of this CIF file, but both crash my program.? > > Other CIF files I have tried from the database load perfectly well.? > > Thanks! > > Tim > > -- > *Timothy D Siegler?*| NDSEG Fellow, Korgel Group > The University of Texas at Austin?| McKetta Department of Chemical Engineering | Cockrell School of Engineering > 100 E. 24th St. Austin, TX 78712 | NHB 6.352 | 512-471-7043 |?tsiegler at utexas.edu ?? > > > _______________________________________________ > 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 tsiegler at utexas.edu Tue Apr 3 17:32:27 2018 From: tsiegler at utexas.edu (Timothy D Siegler) Date: Tue, 3 Apr 2018 16:32:27 +0200 Subject: [Cod-bugs] A certain CIF is crashing the new version of Mercury In-Reply-To: References: Message-ID: Okay, thanks everyone! I'm convinced it's an issue with Mercury. Thanks again! Tim On Tue, Apr 3, 2018 at 3:33 PM, Andrius Merkys wrote: > Dear Timothy, > > the CIF of COD entry 1545320 is syntactically correct according to the CIF > 1.1 syntax. As Mercury is a closed-source program, I can not investigate > the exact cause of the problem with it. Nevertheless, I have checked the > CIF with cif_linguist (https://github.com/COMCIFS/cif_api), CIF > developer's implementation of the CIF parser, to find out that cif_linguist > requires CIF value 'Fc^*^=kFc[1+0.001xFc^2^\l^3^/sin(2\q)]^-1/4^' be > quoted (I have submitted a bug report, https://github.com/COMCIFS/ > cif_api/issues/22). The same reason may be with Mercury. You may try to > remove the CIF line with _refine_ls_extinction_expression data item and > try again to test it. > > Best wishes, > Andrius > > On 04/03/2018 04:07 PM, Timothy D Siegler wrote: > > To whom it may concern: > > I just downloaded the new version of Mercury. In the new version, CIF > #1545320 will not load.I tried using both my old copy and a newly > downloaded copy of this CIF file, but both crash my program. > > Other CIF files I have tried from the database load perfectly well. > > Thanks! > > Tim > > -- > *Timothy D Siegler *| NDSEG Fellow, Korgel Group > The University of Texas at Austin | McKetta Department of Chemical > Engineering | Cockrell School of Engineering > 100 E. 24th St. Austin, TX 78712 > > | NHB 6.352 | 512-471-7043 <(512)%20471-7043> | tsiegler at utexas.edu > > > _______________________________________________ > Cod-bugs mailing listCod-bugs at lists.crystallography.nethttp://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 > > -- *Timothy D Siegler *| NDSEG Fellow, Korgel Group The University of Texas at Austin | McKetta Department of Chemical Engineering | Cockrell School of Engineering 100 E. 24th St. Austin, TX 78712 | NHB 6.352 | 512-471-7043 | tsiegler at utexas.edu -------------- next part -------------- An HTML attachment was scrubbed... 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