<div dir="ltr"><br><br><div class="gmail_quote"><div dir="ltr" class="gmail_attr">---------- Forwarded message ---------<br>From: <b class="gmail_sendername" dir="auto">Antanas Vaitkus</b> <span dir="auto"><<a href="mailto:antanas.vaitkus90@gmail.com">antanas.vaitkus90@gmail.com</a>></span><br>Date: Wed, 11 Dec 2019 at 07:04<br>Subject: Re: [Cod-bugs] special characters (0x1b, 0x07) in CIF files<br>To: Marcin Wojdyr <<a href="mailto:wojdyr@gmail.com">wojdyr@gmail.com</a>><br></div><br><br><div dir="ltr"><div><div><div>Dear Marcin Wojdyr,<br><br></div>thank You for informing us of this issue. The special characters were most likely introduced by the original publisher of the CIF file. For example, the original file of COD entry 4089313 (located at <a href="https://pubs.acs.org/doi/suppl/10.1021/om010651j/suppl_file/om010651j.cif" target="_blank">https://pubs.acs.org/doi/suppl/10.1021/om010651j/suppl_file/om010651j.cif</a>) contains the same syntax errors as the entry in the COD.<br><br></div>Normally, during our automatic deposition workflow such symbols would be detected an encoded using their hex codes (i.e. "#x001B;"). However, in these particular cases, a slightly older version of our software must have been used which did not properly handle some of the lower-number ASCII symbols. We will fix the corrupted files as soon as possible as well as deploy the updated version of the software to avoid such discrepancies in the future.<br><br></div><div>Thanks again for the report.<br></div></div><br><div class="gmail_quote"><div dir="ltr" class="gmail_attr">On Tue, 10 Dec 2019 at 22:46, Marcin Wojdyr <<a href="mailto:wojdyr@gmail.com" target="_blank">wojdyr@gmail.com</a>> wrote:<br></div><blockquote class="gmail_quote" style="margin:0px 0px 0px 0.8ex;border-left:1px solid rgb(204,204,204);padding-left:1ex"><div dir="ltr"><div>Hi,</div><div><br></div><div>I downloaded COD a few days ago and I noticed that some files fail to parse for me because of special characters, most ESC. Below is the full list.</div><div>For example:<br></div><div>_diffrn_radiation_type MoK^[$B%(^[(Ba</div><div>(but ^[ is ESC code 0x07 in the file)</div><div><br></div><div>Do you know what program writes these characters?</div><div><br></div><div>Cheers,</div><div>Marcin<br></div><div><br></div><div>$ time find ../cod/cif/ -name \*.cif | xargs -n1000 ./build/gemmi validate <br>../cod/cif/4/08/93/4089313.cif:58:36(2271): parse error<br>../cod/cif/4/08/93/4089312.cif:58:36(2274): parse error<br>../cod/cif/4/08/93/4089320.cif:119:39(4625): parse error<br>../cod/cif/4/08/93/4089309.cif:59:36(2363): parse error<br>../cod/cif/4/08/93/4089306.cif:59:36(2380): parse error<br>../cod/cif/4/08/93/4089318.cif:54:33(2044): expected value<br>../cod/cif/4/08/93/4089319.cif:55:33(2098): expected value<br>../cod/cif/4/08/93/4089317.cif:58:36(2284): parse error<br>../cod/cif/4/08/93/4089311.cif:59:36(2370): parse error<br>../cod/cif/4/08/93/4089315.cif:58:36(2276): parse error<br>../cod/cif/4/08/93/4089314.cif:58:36(2275): parse error<br>../cod/cif/4/08/93/4089307.cif:59:36(2366): parse error<br>../cod/cif/4/08/93/4089310.cif:59:36(2370): parse error<br>../cod/cif/4/08/93/4089316.cif:58:36(2293): parse error<br>../cod/cif/4/08/93/4089308.cif:59:36(2357): parse error<br>../cod/cif/4/08/97/4089713.cif:60:33(2289): expected value<br>../cod/cif/7/12/54/7125471.cif:68:36(2652): parse error<br>../cod/cif/7/12/54/7125469.cif:70:36(2706): parse error<br><br>real 13m47.423s<br>user 10m38.349s<br>sys 0m38.298s</div></div>
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</blockquote></div><br clear="all"><br>-- <br><div dir="ltr"><div dir="ltr"><div><div>Antanas Vaitkus,<br></div>PhD student at Vilnius University Institute of Biotechnology,<br><span><span><span>room V325, </span></span></span>Saulėtekio al. 7,<br>LT-10257 Vilnius, Lithuania<br></div><div><div><div><div><div dir="ltr"><div><div dir="ltr"><div><div dir="ltr"><br><br></div></div></div></div></div></div></div></div></div></div></div>
</div><br clear="all"><br>-- <br><div dir="ltr" class="gmail_signature" data-smartmail="gmail_signature"><div dir="ltr"><div><div>Antanas Vaitkus,<br></div>PhD student at Vilnius University Institute of Biotechnology,<br><span><span><span>room V325, </span></span></span>Saulėtekio al. 7,<br>LT-10257 Vilnius, Lithuania<br></div><div><div><div><div><div dir="ltr"><div><div dir="ltr"><div><div dir="ltr"><br><br></div></div></div></div></div></div></div></div></div></div></div></div>
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