<div dir="ltr">On Sat, Aug 2, 2014 at 8:36 AM, Alastair Fyfe <span dir="ltr"><<a href="mailto:afyfe@soe.ucsc.edu" target="_blank">afyfe@soe.ucsc.edu</a>></span> wrote:<br><div class="gmail_extra"><div class="gmail_quote">
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<div>I also ran into this recently and was
puzzled about the correct PDB encoding. Using the same residue
number with differing altloc, atom name and element fields seems
straightforward but what should the residue name be ? In my
experience not all PDB-processing software is happy with different
residue names for the same residue number. Is there definitive
PDB documentation for this case?<br></div></div></blockquote><div><br></div><div>This does appear to be permitted by the PDB (in addition to Phenix, of course) - a good example is crambin (1CBN), which has a naturally occurring polymorphism:</div>
<div><pre style="color:rgb(0,0,0);word-wrap:break-word;white-space:pre-wrap">ATOM 352 N ASER A 22 4.909 12.659 -3.127 0.20 3.03 N
ATOM 353 N BSER A 22 4.909 12.659 -3.127 0.20 3.03 N
ATOM 354 CA ASER A 22 6.035 13.459 -2.622 0.20 3.04 C
ATOM 355 CA BSER A 22 6.035 13.459 -2.622 0.20 3.04 C
ATOM 372 N CPRO A 22 4.909 12.659 -3.127 0.60 3.03 N
ATOM 373 CA CPRO A 22 6.035 13.459 -2.622 0.60 3.04 C
<br></pre><pre style="color:rgb(0,0,0);word-wrap:break-word;white-space:pre-wrap"><font face="arial, helvetica, sans-serif">There are other examples of crambin that are numbered differently but this is presumably due to the preferences of the investigator and/or the limitations of the refinement software used. A counter-example is 3QXB, which has mixed metal sites:</font></pre>
<pre style="color:rgb(0,0,0);word-wrap:break-word;white-space:pre-wrap"><br></pre><pre style="color:rgb(0,0,0);word-wrap:break-word;white-space:pre-wrap"><pre style="word-wrap:break-word;white-space:pre-wrap">HETATM 9585 FE A FE A 301 -6.546 23.487 57.436 0.66 26.72 FE
HETATM 9586 MN B MN A 302 -6.549 23.490 57.439 0.34 25.22 MN
<br></pre><pre style="word-wrap:break-word;white-space:pre-wrap"><font face="arial, helvetica, sans-serif">I would say that if software can't handle the first case (same residue number, different residue name) that is a bug, but there doesn't appear to be consensus on the "correct" way to do things. My preference would be to keep the numbering the same but the PDB will accept either convention.</font></pre>
<pre style="word-wrap:break-word;white-space:pre-wrap"><font face="arial, helvetica, sans-serif"><br></font></pre><pre style="word-wrap:break-word;white-space:pre-wrap"><font face="arial, helvetica, sans-serif">-Nat</font></pre>
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