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Hi Guido,</div>
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Yes, there are a few small discrepancies between the AMBER force field and the libraries used for restraints/validation in refinement packages and the wwPDB. That's one of the reasons I try not to describe ISOLDE as a true refinement package (the other being
that it currently doesn't perform B-factor refinement). You'll still want to run a final refinement with your package of choice before depositing to the wwPDB. To help with that, there are the commands:</div>
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isolde write phenixRefineInput</div>
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isolde write phenixRsrInput</div>
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isolde write refmacRestraints</div>
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Just type "usage isolde write" on the command line for more details on their use.</div>
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Best,</div>
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Tristan</div>
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<div id="divRplyFwdMsg" dir="ltr"><font face="Calibri, sans-serif" style="font-size:11pt" color="#000000"><b>From:</b> ChimeraX-users <chimerax-users-bounces@cgl.ucsf.edu> on behalf of Guido Hansen via ChimeraX-users <chimerax-users@cgl.ucsf.edu><br>
<b>Sent:</b> 16 March 2022 17:38<br>
<b>To:</b> chimerax-users@cgl.ucsf.edu <chimerax-users@cgl.ucsf.edu><br>
<b>Subject:</b> [chimerax-users] Bond angles of Arg in ISOLDE</font>
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<p>It seems that the parameterization of ISOLDE's force field differs from the metrics used by the official PBD validation server as I usually get complaints about Arg bond angles from the validation server (see below) even though everything seems fine in ISOLDE.
Is there anything that I can/have to do about that? Or is that something that you would keep as it is and discuss with the PDB people? </p>
<p><img alt="" data-outlook-trace="F:1|T:1" src="cid:11d377ce14f2ac4dcd683be5424ebf5d@biochem.uni-luebeck.de"></p>
<div> - Guido</div>
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