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Hi Pramod,<br>
<br>
please send us model before and after refinement and the map. We
will investigate once we have file and then suggest a solution to
you.<br>
<br>
Pavel<br>
<br>
<div class="moz-cite-prefix">On 9/5/18 04:10, pramod kumar wrote:<br>
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<div><font color="#0B5394">Dear All,</font></div>
<div><font color="#0B5394"><br>
</font></div>
<div><font color="#0B5394">I have a protein-ligand complex
cryo-EM data. The ligand is a primary amine, which at
the neutral pH used during data collection, should be
NH3+ (alkyl-amonium). However, during realspace refine
and despite having provided the CIF file (elbow
generated alkyl-ammonium form), the molecule keeps
"exploding". Instead, the 'NH2 form' (alkyl-amine)
remains stable during refinement and most of the
pdb entries having alkylammonium molecules have modeled
them as the amine form even when they are expected to be
positively charged. Thus, it seems to me that other
groups may have gone through the same difficulties when
trying to refine ammonium groups. </font></div>
<div><font color="#0B5394"><br>
</font></div>
<div><font color="#0B5394">We have already tried:</font></div>
<div><font color="#0B5394">* Ligand build in Lidia and
tried prodrg with error (<font face="monospace" size="3"
color="#CC0000"><span
style="background-color:rgb(238,238,238)"><b>Unrecognised
REFMAC atom type 'HCH3' in input</b></span></font>)</font></div>
<div><font color="#0B5394">* Refmac Acedrg (run201 Error in
wrapper refmac)</font></div>
<div><font color="#0B5394"><br>
</font></div>
<div><font color="#0B5394">Please help me fix this. I could
refine using the amine form, but I know that the amine
form is not right.<br>
</font></div>
<div><font color="#0B5394"><br>
</font></div>
<div><font color="#0B5394">Thank you very much, in advance.</font></div>
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<br class="gmail-Apple-interchange-newline">
<div><br>
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-- <br>
<div dir="ltr" class="gmail_signature"
data-smartmail="gmail_signature">
<div dir="ltr">Promod Jaykar, Ph.D.</div>
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