From robert.mcmeeking at stfc.ac.uk Mon Aug 8 10:24:34 2022 From: robert.mcmeeking at stfc.ac.uk (Robert McMeeking - STFC UKRI) Date: Mon, 8 Aug 2022 07:24:34 +0000 Subject: [Cod-bugs] COD updates In-Reply-To: References: <32fb1a84bffe4ae08896e31c0c6dc67b@stfc.ac.uk> <25011402-3ea5-ddbe-0557-dca9023d56ae@ibt.lt>

Message-ID: Good Morning, Saulius I notice the COD site ( https://www.crystallography.net/cod/) is currently down. Is there a known problems. Best Regards Bob -----Original Message----- From: McMeeking, Robert (STFC,DL,SC) Sent: 22 July 2022 09:54 To: Saulius Gra?ulis Cc: cod-bugs at ibt.lt Subject: RE: COD updates Thanks, Saulius Hopefully the fix will be quite straightforward. Best Regards Bob -----Original Message----- From: Saulius Gra?ulis Sent: 22 July 2022 09:49 To: McMeeking, Robert (STFC,DL,SC) Cc: cod-bugs at ibt.lt Subject: Re: COD updates On 2022-07-22 11:22, Robert McMeeking - STFC UKRI wrote: > I have just noticed that there currently appear to be COD update problems similar to as in the past (see below). > > As I recall this may have been related to making inadvertent changes to protection to files/directories after you performed a system upgrade. Thanks for the e-mail ? yo are write, we have a technical problem, I'm already investigating it and it seems that we have run out of disk space on the scraper machine... It that is the only reason then I'll start the reposition soon and we'll catch up. Sincerely, 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 -- This message has been scanned for viruses and dangerous content by MailScanner, and is believed to be clean. This email and any attachments are intended solely for the use of the named recipients. If you are not the intended recipient you must not use, disclose, copy or distribute this email or any of its attachments and should notify the sender immediately and delete this email from your system. UK Research and Innovation (UKRI) has taken every reasonable precaution to minimise risk of this email or any attachments containing viruses or malware but the recipient should carry out its own virus and malware checks before opening the attachments. UKRI does not accept any liability for any losses or damages which the recipient may sustain due to presence of any viruses. -- 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 Aug 10 08:47:25 2022 From: andrius.merkys at gmail.com (Andrius Merkys) Date: Wed, 10 Aug 2022 08:47:25 +0300 Subject: [Cod-bugs] Electing Anatnas Vaitkus as a voting member of the COD Advisory Board In-Reply-To: References: Message-ID: <7a6387b8-7cdd-31f6-8fc8-4089e9ad0809@gmail.com> Hello, On 2022-07-25 19:13, Saulius Gra?ulis wrote: > Please respond either in this mailing list or use private e-mails of the > COD AB voting members. +1 from me as well! Best wishes, Andrius -- Andrius Merkys Vilnius University Institute of Biotechnology, Saul?tekio al. 7 LT-10257 Vilnius, Lithuania From rowlesmr at gmail.com Sat Aug 13 12:55:50 2022 From: rowlesmr at gmail.com (Matthew Rowles) Date: Sat, 13 Aug 2022 17:55:50 +0800 Subject: [Cod-bugs] I found some errors in CIFs Message-ID: Hi COD people I was playing around with some ideas this week, and when parsing all the CIFs, I got the following errors from my program. They will all relate to errors in how the values of atom coordinates, atomic displacement parameters, or cell parameters are given. I've looked at most of them, and they're fairly obvious in their error. In all cases, this is just the first parsing error encountered; in most files there are more than one. What is the best way to go about fixing them? Regards Matthew file msg cif\7026981.cif could not convert string to float: '6.5*' cif\2003944.cif could not convert string to float: 'O' cif\2002897.cif could not convert string to float: '-' cif\7027704.cif could not convert string to float: '0..049' cif\7217107.cif could not convert string to float: '-' cif\1516392.cif could not convert string to float: '0..0498' cif\2001164.cif could not convert string to float: '.093.' cif\2010104.cif could not convert string to float: '.07.9' cif\4115528.cif could not convert string to float: '0..076' cif\2001895.cif could not convert string to float: '.0.828' cif\2003945.cif could not convert string to float: 'O' cif\2007662.cif could not convert string to float: '0.0634*' cif\2000499.cif could not convert string to float: '.0479{6)' cif\4065647.cif could not convert string to float: '0.11152)' cif\4321917.cif could not convert string to float: '0.0)' cif\4112884.cif could not convert string to float: '0..0460' cif\2101447.cif could not convert string to float: '..114' cif\7012794.cif could not convert string to float: '.0.053' cif\4321125.cif could not convert string to float: ':0.0321' cif\7026982.cif could not convert string to float: '6*' cif\2006442.cif could not convert string to float: '0..0770' cif\2010442.cif could not convert string to float: '0.08*' cif\7009740.cif could not convert string to float: '0..0307' cif\2003869.cif could not convert string to float: '.0458^a^' cif\2003381.cif could not convert string to float: '6*' cif\7051472.cif could not convert string to float: '0..066' cif\2101014.cif could not convert string to float: '.o39' cif\2003699.cif could not convert string to float: '4.0*' cif\2206732.cif could not convert string to float: '0.029m6' cif\2001302.cif could not convert string to float: '0.047*' cif\2006197.cif could not convert string to float: '0..076' cif\4085045.cif could not convert string to float: '0..059' cif\2007409.cif could not convert string to float: '0..0535' cif\2009533.cif could not convert string to float: '/' cif\2007301.cif could not convert string to float: '' cif\4320747.cif could not convert string to float: 'H' cif\4320905.cif could not convert string to float: '0..0629' cif\2007048.cif could not convert string to float: '0.0393*' cif\4322860.cif could not convert string to float: '0..055' cif\2003192.cif could not convert string to float: '0.08*' cif\4322021.cif could not convert string to float: '0..073' cif\2006384.cif could not convert string to float: '0..131' cif\4315383.cif could not convert string to float: '0.0.99' cif\4300081.cif could not convert string to float: '0.l09' cif\7027965.cif could not convert string to float: '0..037' cif\4061854.cif could not convert string to float: '0._61' cif\4300051.cif could not convert string to float: '0..0565' cif\2005964.cif could not convert string to float: '4.4*' cif\2009883.cif could not convert string to float: '.046.5' cif\2007654.cif could not convert string to float: '0.0494*' cif\4323741.cif could not convert string to float: '0..0283' cif\4322390.cif could not convert string to float: '0..115' cif\7111128.cif could not convert string to float: '0..091' cif\2005961.cif could not convert string to float: "C1'" cif\4333084.cif could not convert string to float: '0.09817)' cif\2009384.cif could not convert string to float: 'H91' cif\4320033.cif could not convert string to float: '..0794' cif\7027705.cif could not convert string to float: '0..056' cif\2002898.cif could not convert string to float: '-' cif\4322414.cif could not convert string to float: '0..0266' cif\3500007.cif could not convert string to float: '0.O1D' cif\2007253.cif could not convert string to float: '0..0684' cif\2005907.cif could not convert string to float: '0.0962*' cif\4115907.cif could not convert string to float: '0..0486' cif\4322396.cif could not convert string to float: '0..042' cif\7009739.cif could not convert string to float: '0..0477' cif\2101312.cif could not convert string to float: '6.0*' cif\7702612.cif could not convert string to float: '16*' -- 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... 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