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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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cite="mid:CAH3K_eyekNyxPXJ+DHtgWeFFdf+hsU04AZ-KO8F9vpYOG6G5RQ@mail.gmail.com">
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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>
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          <div dir="ltr">Promod Jaykar, Ph.D.</div>
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