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<pre class="western" style="margin-bottom: 0.2in">Dear phenix-development Team,
when is it advantageous to use automatic linking over supplying a .params file with the link parameters defined to refine links?
I thought that automatic linking will recognize the kind of link by itself and then look for the restraints itself. But it seems not to do,
because it is not complaining that there are still hydrogens in the sugar moeity which should not be there after the link has formed.
This brings me to my second questions. Is there a way to automatically remove the hydrogens which should not be there anymore after the bond has formed. Or tell reduce that it should not add hydrogens at the link?
Thanks in advance.
Best Regards
Georg.
</pre>
<h2 class="western" style="margin-top: 0in; margin-bottom: 0.2in">
<font color="#000080"><span lang="zxx"><a
href="http://www.phenix-online.org/documentation/reference/refinement.html#id47"><span
style="font-variant: normal"><font color="#000000"><span
style="text-decoration: none"><font face="Verdana,
Helvetica, Arial, sans-serif"><font size="4"><span
style="font-style: normal">Automatic
linking</span></font></font></span></font></span></a></span></font></h2>
<p class="western"><span style="font-variant: normal"><font
color="#000000"><font face="Verdana, Helvetica, Arial,
sans-serif"><font style="font-size: 10pt" size="2"><span
style="font-style: normal"><span style="font-weight:
normal">phenix.refine
has an automatic option for generating links </span></span></font></font></font></span><em><span
style="font-variant: normal"><font color="#000000"><font
face="Verdana, Helvetica, Arial, sans-serif"><font
style="font-size: 10pt" size="2"><span
style="font-style: normal"><span style="font-weight:
normal">within
the same chain</span></span></font></font></font></span></em><span
style="font-variant: normal"><font color="#000000"><font
face="Verdana, Helvetica, Arial, sans-serif"><font
style="font-size: 10pt" size="2"><span style="font-style:
normal"><span style="font-weight: normal">.
It will look for carbohydrate links, both within the
sugar polymer
and linking to the protein. Covalent bonded ligands
can also be
linked with this option.</span></span></font></font></font></span></p>
<p class="western" style="font-variant: normal; font-style: normal;
font-weight: normal">
<font face="Verdana, Helvetica, Arial, sans-serif"><font
style="font-size: 10pt" size="2">automatic_linking.link_all
= True</font></font></p>
<p class="western" style="font-variant: normal; font-style: normal;
font-weight: normal">
<font face="Verdana, Helvetica, Arial, sans-serif"><font
style="font-size: 10pt" size="2">There
are a number of parameters that allow the tailoring of the
various
bond class cutoffs.</font></font></p>
<pre class="western" style="font-variant: normal; font-style: normal; font-weight: normal">automatic_linking {
<span style="font-style: normal"><span style="font-weight: normal">metal_coordination_cutoff = 3.5</span></span>
<span style="font-style: normal"><span style="font-weight: normal">amino_acid_bond_cutoff = 1.9</span></span>
<span style="font-style: normal"><span style="font-weight: normal">rna_dna_bond_cutoff = 3.5</span></span>
<span style="font-style: normal"><span style="font-weight: normal">inter_residue_bond_cutoff = 2.5</span></span>
<span style="font-style: normal"><span style="font-weight: normal">carbohydrate_bond_cutoff = 1.99</span></span>
}</pre>
<p class="western" style="font-variant: normal; font-style: normal;
font-weight: normal">
<font face="Verdana, Helvetica, Arial, sans-serif"><font
style="font-size: 10pt" size="2">There
are also options within the automatic_linking scope for
various bond
length cutoffs.</font></font></p>
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