https://feig.bch.msu.edu/mmtsb/mwiki-mmtsb/index.php?action=history&feed=atom&title=Selection_Syntax 2026-05-22T01:47:16Z Revision history for this page on the wiki MediaWiki 1.34.2 https://feig.bch.msu.edu/mmtsb/mwiki-mmtsb/index.php?title=Selection_Syntax&diff=1529&oldid=prev 2007-09-03T20:21:57Z

<p></p> <table class="diff diff-contentalign-left" data-mw="interface"> <col class="diff-marker" /> <col class="diff-content" /> <col class="diff-marker" /> <col class="diff-content" /> <tr class="diff-title" lang="en"> <td colspan="2" style="background-color: #fff; color: #222; text-align: center;">←Older revision</td> <td colspan="2" style="background-color: #fff; color: #222; text-align: center;">Revision as of 20:21, 3 September 2007</td> </tr><tr><td colspan="2" class="diff-lineno" id="mw-diff-left-l16" >Line 16:</td> <td colspan="2" class="diff-lineno">Line 16:</td></tr> <tr><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"></td><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"></td></tr> <tr><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>   A:                    (chain A)</div></td><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>   A:                    (chain A)</div></td></tr> <tr><td colspan="2"> </td><td class='diff-marker'>+</td><td style="color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;"><div><ins style="font-weight: bold; text-decoration: none;">  PROA:                  (segid PROA)</ins></div></td></tr> <tr><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>   A+B:                  (chain A or B)</div></td><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>   A+B:                  (chain A or B)</div></td></tr> <tr><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>   ^A:                    (not chain A)</div></td><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>   ^A:                    (not chain A)</div></td></tr> <tr><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>   !A+B:                  (neither chain A nor B)</div></td><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>   !A+B:                  (neither chain A nor B)</div></td></tr> <tr><td class='diff-marker'>−</td><td style="color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #ffe49c; vertical-align: top; white-space: pre-wrap;"><div> </div></td><td class='diff-marker'>+</td><td style="color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;"><div><ins class="diffchange diffchange-inline">  </ins></div></td></tr> <tr><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>* select residue(s):</div></td><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>* select residue(s):</div></td></tr> <tr><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"></td><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"></td></tr> </table>

35.9.97.235 https://feig.bch.msu.edu/mmtsb/mwiki-mmtsb/index.php?title=Selection_Syntax&diff=1513&oldid=prev 2006-08-14T02:48:46Z

<p></p> <p><b>New page</b></p><div>* general format:<br /> <br /> [chain]:[residues].[atoms]<br /> <br /> * an entire expression can be negated with !<br /> * a chain/segment/atom/residue selection is negated with ^<br /> * + corresponds to logical OR operator in specifying multiple residues/atoms<br /> * / corresponds to logical AND operator<br /> * ? finds first occurence of amino acid sequence<br /> <br /> * entirely different selections can be combined with _ (logical OR)<br /> <br /> Examples:<br /> <br /> * select chain(s):<br /> <br /> A: (chain A)<br /> A+B: (chain A or B)<br /> ^A: (not chain A)<br /> !A+B: (neither chain A nor B)<br /> <br /> * select residue(s):<br /> <br /> PRO (proline) <br /> GUA+ADE (guanine or adenine)<br /> 2-5 (residues 2 through 5)<br /> hydrophobic (hydrophobic residues)<br /> hetero/^HOH (hetero groups except for HOH)<br /> <br /> * select atoms(s):<br /> <br /> CA (Calpha)<br /> CA+CB (Calpha or Cbeta)<br /> <br /> * combined residues/atoms:<br /> <br /> GUA.O1P (O1P of guanine residues)<br /> ALA+GLY.CA (Calpha of alanine or glycine)<br /> <br /> * combined chain/residues/atoms:<br /> <br /> A:GUA.base (nucleotide base atoms of guanines in chain A)<br /> A:GUA/10-12.base (guanine base atoms within residues 10 to 12 from chain A)<br /> <br /> * different sets <br /> <br /> A:GUA.base_B:CYT.base (guanine base atoms from chain A plus cytosine base atoms from chain B)<br /> <br /> * search for sequence<br /> <br /> @LKYTA (find part of structure that matches sequence) <br /> @LK/^10-20.CA (sequence LK except for residues 10 through 20, Calpha atoms only)<br /> <br /> * complete list of supported residue selections:<br /> <br /> [residue number range]<br /> [residue name]<br /> peptide<br /> protein<br /> basic<br /> acidic<br /> charged<br /> hydrophobic<br /> polar<br /> nucleic<br /> purine<br /> pyrimidine<br /> water<br /> metal<br /> ion<br /> hetero<br /> <br /> * complete list of supported atom selections:<br /> <br /> [atom name]<br /> backbone<br /> sidechain<br /> sugar<br /> base<br /> heavy<br /> hydrogen<br /> oxygen<br /> nitrogen<br /> carbon<br /> sulfur<br /> phosphorus</div>

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