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<p><span style="font-family: arial, helvetica, sans-serif; font-size: 12pt;">Hi ChimeraX-users,</span></p>
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<p><span style="font-family: arial, helvetica, sans-serif; font-size: 12pt;">I have used recently the mmaker cmd to align two pdb each have multiple chains as below.</span></p>
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<p class="western"><span style="font-size: 12pt; font-family: arial, helvetica, sans-serif;">mmaker #12/L,M,N to #5/S,A,B matrix blosum-62 showAlignment true</span></p>
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<p class="western"><span style="font-size: 12pt; font-family: arial, helvetica, sans-serif;">But the sequence view shows only the alignment of chain L and S. </span></p>
<p class="western"><span style="font-size: 12pt; font-family: arial, helvetica, sans-serif;">1. I would like to have aligned sequences of all chains used in mmaker alignement.</span></p>
<p class="western"><span style="font-size: 12pt; font-family: arial, helvetica, sans-serif;">2. Is it possible to open the saved RMSD header values in a file later just to color the pdb?</span></p>
<p class="western"><span style="font-size: 12pt; font-family: arial, helvetica, sans-serif;">3. Do mmaker align entire pdb based on selected chains and Can calculate RMSD for all residues in the pdb?</span></p>
<p class="western"><span style="font-size: 12pt; font-family: arial, helvetica, sans-serif;">4. I also would like to change the displayed text for the sequence name. Presently it puts the filename as sequence name.</span></p>
<p class="western"><span style="font-size: 12pt; font-family: arial, helvetica, sans-serif;"> [similar to 'Edit sequence name' in the sequence viewer in chimera]</span></p>
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<p class="western"><span style="font-size: 12pt; font-family: arial, helvetica, sans-serif;">Please let me know how this can be done.</span></p>
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<p class="western"><span style="font-size: 12pt; font-family: arial, helvetica, sans-serif;">thank you very much</span></p>
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<p class="western"><span style="font-size: 12pt; font-family: arial, helvetica, sans-serif;">with kind regards</span></p>
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<p class="western"><span style="font-size: 12pt; font-family: arial, helvetica, sans-serif;">Mani.</span></p>
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