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<p class="MsoNormal"><span style="font-size:11.0pt">Hi Phil, the pdb file represents the asymmetric unit of the crystal, the smallest unit that can be propagated by the crystal symmetry operators to regenerate the crystal lattice. It is common for proteins
to crystallize in a form that also contains noncrystallographic symmetry, ie symmetry operations that can’t be propagated through the crystal lattice. Sometimes this is biologically significant, eg in the case of a homoassembly, but other times it is simply
the lowest energy way to fill a lattice. In such a case, multiple copies of the protein must be modeled to fill the asymmetric unit. Usually the copies are identical, or nearly so.<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt"><o:p> </o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt">In chimeraX, you can select copies of chains you aren’t interested in and either hide or delete them.<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt"><o:p> </o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt">Best wishes<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt">Kevin<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt"><o:p> </o:p></span></p>
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<p class="MsoNormal" style="margin-bottom:12.0pt"><b><span style="font-size:12.0pt;color:black">From:
</span></b><span style="font-size:12.0pt;color:black">ChimeraX-users <chimerax-users-bounces@cgl.ucsf.edu> on behalf of McClean, Phillip via ChimeraX-users <chimerax-users@cgl.ucsf.edu><br>
<b>Date: </b>Wednesday, November 9, 2022 at 4:47 PM<br>
<b>To: </b>chimerax-users@cgl.ucsf.edu <chimerax-users@cgl.ucsf.edu><br>
<b>Subject: </b>[chimerax-users] .pdb from Protein Data Bank has more chains than expected<o:p></o:p></span></p>
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<p class="MsoNormal" style="background:white"><span style="font-size:12.0pt;color:black">Hi Everyone,<o:p></o:p></span></p>
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<p class="MsoNormal" style="background:white"><span style="font-size:12.0pt;color:black"><o:p> </o:p></span></p>
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<p class="MsoNormal" style="background:white"><span style="font-size:12.0pt;color:black">I downloaded the 7FDL .pdb from the Protein Data Bank. I was expecting just two chains (it is a heteromeric complex), but I found 12 chains in the file (A-L). I was expecting
two chains because the manuscript suggested they were just modeling protein fragments of the two protein. It appears that chains that A,C,E,G,I,K are multiple models of one fragment, while chains B,D,F,H,J,L are multiple models of the second fragment.<o:p></o:p></span></p>
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<p class="MsoNormal" style="background:white"><span style="font-size:12.0pt;color:black"><o:p> </o:p></span></p>
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<p class="MsoNormal" style="background:white"><span style="font-size:12.0pt;color:black">Two questions. Why are multiple structures reported, and how to I visualize just two fragments at the same time, for example A and B.<o:p></o:p></span></p>
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<p class="MsoNormal" style="background:white"><span style="font-size:12.0pt;color:black"><o:p> </o:p></span></p>
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<p class="MsoNormal" style="background:white"><span style="font-size:12.0pt;color:black">I have attached the .pdb file.<o:p></o:p></span></p>
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<p class="MsoNormal" style="background:white"><span style="font-size:12.0pt;color:black"><o:p> </o:p></span></p>
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<p class="MsoNormal" style="background:white"><span style="font-size:12.0pt;color:black">Thanks for any advise.<o:p></o:p></span></p>
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<p class="MsoNormal" style="background:white"><span style="font-size:12.0pt;color:black"><o:p> </o:p></span></p>
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<p class="MsoNormal" style="background:white"><span style="font-size:12.0pt;color:black">Phil McClean<o:p></o:p></span></p>
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<p class="MsoNormal" style="background:white"><span style="font-size:12.0pt;color:black"><o:p> </o:p></span></p>
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<p class="MsoNormal" style="background:white"><span style="font-size:12.0pt;color:black"><o:p> </o:p></span></p>
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