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<p class="MsoNormal"><span style="font-size:11.0pt;mso-fareast-language:EN-US">Dear ClAuS,
<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 is very easy and works ! For myosins we always use a Gelly file for the Mg2+ coordination, so I just needed to add the line there.<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">Sure it’ll be better to have it corrected in the next release, but for the moment it’ll do it, no problem.
<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">Thank you very much, and have a great week,<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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<div>
<p class="MsoNormal"><span style="font-size:11.0pt;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;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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<p class="MsoNormal" style="margin-bottom:12.0pt"><b><span style="font-size:12.0pt;font-family:"Aptos",sans-serif;color:black">De :
</span></b><span style="font-size:12.0pt;font-family:"Aptos",sans-serif;color:black">buster-discuss <buster-discuss-bounces@globalphasing.com> de la part de buster-discuss-request@globalphasing.com <buster-discuss-request@globalphasing.com><br>
<b>Date : </b>vendredi, 2 février 2024 à 16:26<br>
<b>À : </b>buster-discuss@globalphasing.com <buster-discuss@globalphasing.com><br>
<b>Objet : </b>buster-discuss Digest, Vol 76, Issue 2<o:p></o:p></span></p>
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<br>
Today's Topics:<br>
<br>
1. Re: Big trouble with MLY (Kikuti Carlos)<br>
2. Re: Big trouble with MLY (ClAuS Flensburg)<br>
<br>
<br>
----------------------------------------------------------------------<br>
<br>
Message: 1<br>
Date: Fri, 2 Feb 2024 11:52:55 +0000<br>
From: Kikuti Carlos <Carlos.Kikuti@curie.fr><br>
To: "buster-discuss@globalphasing.com"<br>
<buster-discuss@globalphasing.com><br>
Subject: Re: [buster-discuss] Big trouble with MLY<br>
Message-ID:<br>
<PR1P264MB34786F5F0069B94196DAD09387422@PR1P264MB3478.FRAP264.PROD.OUTLOOK.COM><br>
<br>
Content-Type: text/plain; charset="windows-1252"<br>
<br>
Hey Phil and Rohan,<br>
<br>
Thank you for your replies. I have only 2 copies of MLY.cif in the computer, one is in $CCP4/lib/data/monomers/m, the other one is in Coot’s directory under $CCP4, and they are identical. So I guess Buster is taking the one from $CCP4, right?<br>
<br>
If that’s correct, then yes, it is already as peptide:<br>
MLY MLY N-DIMETHYL-LYSINE peptide 30 12 .<br>
<br>
<br>
* Which is curious because, also for M3L for which the TER line is not added, Buster will always convert them to HETATM, even if you manually edit the pdb file.<br>
<br>
In Coot, the peptide bonds around the newly added MLY look OK, but I created the LINKs as suggested by Rohan anyways:<br>
LINK N MLY A 189 C THR A 188 1555 1555<br>
LINK C MLY A 189 N LYS A 190 1555 1555<br>
<br>
But when Buster takes it up, it is still creating the TER line at aa 188… Even if I tell it Pdb2Tnt_RunAdjustLNNN=yes<br>
<br>
I believe this is something within the Buster/TNT/Gelly code, but my skills are not that developed to find where exactly… I wish there was a keyword like CreateTERLineBeforeSpecialResidue=no …<br>
<br>
Anyways, for the moment I using a workaround that I’m describing for records, for when other people face the same issue:<br>
<br>
1. Modify the refine.pdb: remove the TER line before the special amino acid;<br>
2. Convert it to mmcif (for instance with <a href="https://mmcif.pdbj.org/converter/">
https://mmcif.pdbj.org/converter/</a> );<br>
3. Download the resulting mmcif file and submit that to Validate.<br>
<br>
This is much easier (at least to me) than modifying directly the BUSTER_model.cif, which requires many more changes (all those exclamation marks).<br>
<br>
Well, I’m still on the lookout for a real solution.<br>
<br>
All the best,<br>
<br>
---------------------------------------------------<br>
Carlos KIKUTI, PhD<br>
UMR144 - CNRS - Institut Curie<br>
Pavillon Trouillet Rossignol<br>
26 Rue d’Ulm - 75005 Paris, France<br>
carlos.kikuti@curie.fr<mailto:carlos.kikuti@curie.fr><br>
<br>
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------------------------------<br>
<br>
Message: 2<br>
Date: Fri, 2 Feb 2024 15:25:38 +0000<br>
From: ClAuS Flensburg <claus@globalphasing.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] Big trouble with MLY<br>
Message-ID: <20240202152538.GN25590@laue.globalphasing.com><br>
Content-Type: text/plain; charset=us-ascii<br>
<br>
Dear Carlos,<br>
<br>
On Fri, Feb 02, 2024 at 11:52:55AM +0000, Kikuti Carlos wrote:<br>
> Hey Phil and Rohan,<br>
> <br>
> Thank you for your replies. I have only 2 copies of MLY.cif in the computer, one is in $CCP4/lib/data/monomers/m, the other one is in Coot?s directory under $CCP4, and they are identical. So I guess Buster is taking the one from $CCP4, right?<br>
> <br>
> If that?s correct, then yes, it is already as peptide:<br>
> MLY MLY N-DIMETHYL-LYSINE peptide 30 12 .<br>
> <br>
> <br>
> * Which is curious because, also for M3L for which the TER line is not added, Buster will always convert them to HETATM, even if you manually edit the pdb file.<br>
> <br>
> In Coot, the peptide bonds around the newly added MLY look OK, but I created the LINKs as suggested by Rohan anyways:<br>
> LINK N MLY A 189 C THR A 188 1555 1555<br>
> LINK C MLY A 189 N LYS A 190 1555 1555<br>
> <br>
> But when Buster takes it up, it is still creating the TER line at aa 188? Even if I tell it Pdb2Tnt_RunAdjustLNNN=yes<br>
> <br>
> I believe this is something within the Buster/TNT/Gelly code, but my skills are not that developed to find where exactly? I wish there was a keyword like CreateTERLineBeforeSpecialResidue=no ?<br>
> <br>
> Anyways, for the moment I using a workaround that I?m describing for records, for when other people face the same issue:<br>
> <br>
> 1. Modify the refine.pdb: remove the TER line before the special amino acid;<br>
> 2. Convert it to mmcif (for instance with <a href="https://mmcif.pdbj.org/converter/">
https://mmcif.pdbj.org/converter/</a> );<br>
> 3. Download the resulting mmcif file and submit that to Validate.<br>
> <br>
> This is much easier (at least to me) than modifying directly the BUSTER_model.cif, which requires many more changes (all those exclamation marks).<br>
> <br>
> Well, I?m still on the lookout for a real solution.<br>
<br>
BUSTER will issue TER record prior to components that are not<br>
considered to be part of a polymer. The membership of the polymer set<br>
is generally defined in the files sets.dat and exoticaa.dat. Specifically<br>
<br>
...<br>
NOTE BUSTER_DICT_ECHO Polymer: for PDB TER record and mmCIF pdbx_refine_tls_group treatment.<br>
NOTE BUSTER_DICT_SET Polymer = Protein + Nucleic<br>
...<br>
<br>
The easiest method to fix your issue with TER records would be to<br>
append MLY to the Polymer set like this:<br>
<br>
cat > add-mly-to-polymer-set.dat <<EOF<br>
NOTE BUSTER_DICT_SET Polymer = Polymer + {RESTYPE MLY}<br>
EOF<br>
<br>
and then run BUSTER with<br>
<br>
refine -Gelly add-mly-to-polymer-set.dat ...<br>
<br>
Does this do what you expect it to do?<br>
<br>
<br>
Also, note how M3L is already in the ExoticAA set which is why there<br>
is no TER record for those. We should make the content of exoticaa.dat<br>
consistent, and will make sure that this is done in the next release.<br>
<br>
<br>
Best regards,<br>
<br>
ClAuS (for BUSTER Developers)<br>
<br>
<br>
------------------------------<br>
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End of buster-discuss Digest, Vol 76, Issue 2<br>
*********************************************<o:p></o:p></span></p>
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