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<p class="MsoNormal"><span style="font-size:11.0pt;mso-fareast-language:EN-US">Dear Marcin,<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;mso-fareast-language:EN-US"><o:p> </o:p></span></p>
<p class="MsoNormal"><span lang="EN-US" style="font-size:11.0pt;mso-fareast-language:EN-US">That’s fine, then. I agree it could be something related to the internal change back then. Our student confirms she can run Validate without modifying the mmcifs now.<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US" style="font-size:11.0pt;mso-fareast-language:EN-US"><o:p> </o:p></span></p>
<p class="MsoNormal"><span lang="EN-US" style="font-size:11.0pt;mso-fareast-language:EN-US">Thanks to you and Clemens for having checked.<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US" style="font-size:11.0pt;mso-fareast-language:EN-US"><o:p> </o:p></span></p>
<p class="MsoNormal"><span lang="EN-US" style="font-size:11.0pt;mso-fareast-language:EN-US">All the best,<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US" style="font-size:11.0pt;mso-fareast-language:EN-US"><o:p> </o:p></span></p>
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<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:black">---------------------------------------------------<br>
Carlos KIKUTI, PhD<br>
UMR144 - CNRS - Institut Curie<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:black">Pavillon Trouillet Rossignol <br>
26 Rue d’Ulm - 75005 Paris, France<br>
<a href="mailto:carlos.kikuti@curie.fr" title="mailto:carlos.kikuti@curie.fr"><span style="color:#0563C1">carlos.kikuti@curie.fr</span></a><o:p></o:p></span></p>
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----------------------------------------------------------------------<br>
<br>
Message: 1<br>
Date: Thu, 5 Dec 2024 14:36:21 +0100<br>
From: Marcin Wojdyr <wojdyr@gmail.com><br>
To: Kikuti Carlos <Carlos.Kikuti@curie.fr><br>
Cc: "buster-discuss@globalphasing.com"<br>
<buster-discuss@globalphasing.com><br>
Subject: Re: [buster-discuss] PDB Validate doesn't like mmCif file<br>
from Buster<br>
Message-ID:<br>
<CACaHzQVk5gg4-HHcs0xU=NFvtgUpkM+E-FSWX8S9FzyngfUnbA@mail.gmail.com><br>
Content-Type: text/plain; charset="UTF-8"<br>
<br>
Hi Carlos,<br>
<br>
Thanks for forwarding the discussion.<br>
</span><span style="font-size:11.0pt">I also couldn't reproduce it. The lines that the PDB person advised to<br>
remove have never caused any problems, so I'd guess it was a red<br>
herring. Perhaps there was some intermittent problem that later went<br>
away. If you'd use the validation server again, don't bother with<br>
removing anything from mmcif. But of course if you'd see any issues<br>
again we'd be happy to investigate it further.<br>
<br>
As for running the validation locally, the pipelines that the PDB uses<br>
for validation and deposition aren't fully open. I don't know if it'd<br>
be possible to reproduce them. Some older programs used in these<br>
pipelines are available on the RCSB website and occasionally new<br>
versions are uploaded there. There are also some programs maintained<br>
in Github repositories. However, that's probably not all the software<br>
that is used and I don't have a complete picture of what is running on<br>
the PDB servers.<br>
<br>
The issue you reported was from mid October. Coincidentally, a week or<br>
two before that I reported an unrelated issue to the PDB. In response,<br>
one of the PDB developers released a new version of MAXIT (the program<br>
that the PDB uses to read and convert coordinate files). That was on<br>
Oct 11. Probably the validation service was at some point updated to<br>
use that new version, but according to another PDB person OneDep<br>
hasn't been updated yet. Tracking such problems often feels like<br>
navigating in the dark.<br>
<br>
Best wishes,<br>
Marcin<br>
<br>
On Wed, Dec 4, 2024 at 1:20</span><span style="font-size:11.0pt;font-family:"Arial",sans-serif"> </span><span style="font-size:11.0pt">PM Kikuti Carlos via buster-discuss<br>
<buster-discuss@globalphasing.com> wrote:<br>
><br>
> Hello !<br>
><br>
><br>
><br>
> Marcin, I’ve just sent it to your e-mail, thank you.<br>
><br>
><br>
><br>
> If you or anybody else has ideas concerning the second part: “To ask if you have other suggestions of routines, other than uploading to Validate for this kind of pre-submission test? We use the validation tools in Coot and Molprobity, but for some reason
the criteria and the calculated maps are not exactly the same as for the PDB… It would be much easier to have this validation running locally, just to avoid the uploading interface.”<br>
><br>
> … I’m all ears.<br>
><br>
><br>
><br>
> Best,<br>
><br>
><br>
><br>
> ---------------------------------------------------<br>
> Carlos KIKUTI, PhD<br>
> UMR144 - CNRS - Institut Curie<br>
><br>
> Pavillon Trouillet Rossignol<br>
> 26 Rue d’Ulm - 75005 Paris, France<br>
> carlos.kikuti@curie.fr<br>
><br>
><br>
> Message: 2<br>
> Date: Tue, 3 Dec 2024 17:57:58 +0100<br>
> From: Marcin Wojdyr <wojdyr@gmail.com><br>
> To: Kikuti Carlos <Carlos.Kikuti@curie.fr><br>
> Cc: "buster-discuss@globalphasing.com"<br>
> <buster-discuss@globalphasing.com>, Glaser Camille<br>
> <camille.glaser@curie.fr><br>
> Subject: Re: [buster-discuss] PDB Validate doesn't like mmCif file<br>
> from Buster<br>
> Message-ID:<br>
> <CACaHzQXvKWhbkFHYUvz4ZFqBnwhABALrovAKWTawK8+dWs4K-A@mail.gmail.com><br>
> Content-Type: text/plain; charset="UTF-8"<br>
><br>
> Hello Carlos,<br>
><br>
> Thanks for reporting this problem. I don't know what went wrong here.<br>
> It'd be good to track it down, but I'm not able to reproduce it.<br>
><br>
> How did you discuss it with the PDB people? If by email, could you<br>
> forward it to me?<br>
><br>
> Thanks,<br>
> Marcin<br>
> *********************************************<br>
><br>
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