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<p class="MsoNormal"><span style="font-size:11.0pt;color:black;mso-fareast-language:EN-GB">Hi,</span><span style="color:black;mso-fareast-language:EN-GB"><o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;color:black;mso-fareast-language:EN-GB"> </span><span style="color:black;mso-fareast-language:EN-GB"><o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;color:black;mso-fareast-language:EN-GB">I am having trouble excluding bonding terms between a partially bound ligand and a disordered side chain. I used (several years ago) to just type</span><span style="color:black;mso-fareast-language:EN-GB"><o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;color:black;mso-fareast-language:EN-GB"> </span><span style="color:black;mso-fareast-language:EN-GB"><o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;color:black;mso-fareast-language:EN-GB">EXCLUDE D|121 E|1 </span><span style="color:black;mso-fareast-language:EN-GB"><o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;color:black;mso-fareast-language:EN-GB"> </span><span style="color:black;mso-fareast-language:EN-GB"><o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;color:black;mso-fareast-language:EN-GB">At the bottom of the restraints.dat (the molprobity CB deviation fixer) file and this seemed to work, but now it gets ignored and the two residues are forced apart, rather
than overlapping.</span><span style="color:black;mso-fareast-language:EN-GB"><o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;color:black;mso-fareast-language:EN-GB"> </span><span style="color:black;mso-fareast-language:EN-GB"><o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;color:black;mso-fareast-language:EN-GB">I also tried to add it directly on the command line with</span><span style="color:black;mso-fareast-language:EN-GB"><o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;color:black;mso-fareast-language:EN-GB"> </span><span style="color:black;mso-fareast-language:EN-GB"><o:p></o:p></span></p>
<p class="MsoNormal" style="background:white"><span style="font-size:11.0pt;color:black;mso-fareast-language:EN-GB">refine -m ………. -p refine refine-coot-0.pdb ExcludeBadContacts="EXCLUDE A|121 E|2; EXCLUDE B|121 E|1; EXCLUDE B|281 D|281"</span><span style="font-size:8.5pt;font-family:Menlo;color:black;mso-fareast-language:EN-GB"><o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;color:black;mso-fareast-language:EN-GB"> </span><span style="color:black;mso-fareast-language:EN-GB"><o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;color:black;mso-fareast-language:EN-GB">but again this is ignored.</span><span style="color:black;mso-fareast-language:EN-GB"><o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;color:black;mso-fareast-language:EN-GB"> </span><span style="color:black;mso-fareast-language:EN-GB"><o:p></o:p></span></p>
<p class="MsoNormal" style="background:white"><span style="font-size:8.5pt;font-family:Menlo;color:black;mso-fareast-language:EN-GB"> <b>WARNING</b> : some warning messages received - details below<o:p></o:p></span></p>
<p class="MsoNormal" style="background:white"><span style="font-size:8.5pt;font-family:Menlo;color:black;mso-fareast-language:EN-GB"> <o:p></o:p></span></p>
<p class="MsoNormal" style="background:white"><span style="font-size:8.5pt;font-family:Menlo;color:black;mso-fareast-language:EN-GB"> WARNING: Have |delta/sigma| deviations > 5.0 sigma. Number of outliers for each term: <o:p></o:p></span></p>
<p class="MsoNormal" style="background:white"><span style="font-size:8.5pt;font-family:Menlo;color:black;mso-fareast-language:EN-GB"> WARNING: 1 bond lengths. Worst is 8.0 sigs 1.49 Angs A|283:C.B(GLU)=A|284:N(PRO)<o:p></o:p></span></p>
<p class="MsoNormal" style="background:white"><span style="font-size:8.5pt;font-family:Menlo;color:black;mso-fareast-language:EN-GB"> WARNING: 5 bond angles. Worst is 7.6 sigs 130.73 degs A|283:C.B(GLU)=A|284:N(PRO)=A|284:CA(PRO)<o:p></o:p></span></p>
<p class="MsoNormal" style="background:white"><span style="font-size:8.5pt;font-family:Menlo;color:black;mso-fareast-language:EN-GB"> WARNING: 1 planes. Worst is 6.4 sigs 0.13 Angs E|1:C3=C4=N2=C5 (LIG)<o:p></o:p></span></p>
<p class="MsoNormal" style="background:white"><span style="font-size:8.5pt;font-family:Menlo;color:black;mso-fareast-language:EN-GB"> WARNING: 21 idealD contacts. Worst 15.9 sigs 1.41 Angs B|121:CZ.A(TYR)=E|2:C7(LIG)<o:p></o:p></span></p>
<p class="MsoNormal" style="background:white"><span style="font-size:8.5pt;font-family:Menlo;color:black;mso-fareast-language:EN-GB"> WARNING: 4 Bcorrel. Worst is 9.7 sigs -24.12 Angs^2 B|3:CA=CB (ALA)<o:p></o:p></span></p>
<p class="MsoNormal" style="background:white"><span style="font-size:8.5pt;font-family:Menlo;color:black;mso-fareast-language:EN-GB"> WARNING: Could be a bad contact but may well be an unrecognized link from<o:p></o:p></span></p>
<p class="MsoNormal" style="background:white"><span style="font-size:8.5pt;font-family:Menlo;color:black;mso-fareast-language:EN-GB"> protein to HETATM residue? It is possible restraints have not been<o:p></o:p></span></p>
<p class="MsoNormal" style="background:white"><span style="font-size:8.5pt;font-family:Menlo;color:black;mso-fareast-language:EN-GB"> properly set up.<o:p></o:p></span></p>
<p class="MsoNormal" style="background:white"><span style="font-size:8.5pt;font-family:Menlo;color:black;mso-fareast-language:EN-GB"> If you want BUSTER to regard this as a bond try adding the<o:p></o:p></span></p>
<p class="MsoNormal" style="background:white"><span style="font-size:8.5pt;font-family:Menlo;color:black;mso-fareast-language:EN-GB"> following card before the CRYST1 line in the input pdb file:<o:p></o:p></span></p>
<p class="MsoNormal" style="background:white"><span style="font-size:8.5pt;font-family:Menlo;color:black;mso-fareast-language:EN-GB"> LINK CE1ATYR B 121 C7 LIG E 2 1555 1555 1.67 <o:p></o:p></span></p>
<p class="MsoNormal" style="background:white"><span style="font-size:8.5pt;font-family:Menlo;color:black;mso-fareast-language:EN-GB"> WARNING: Could be a bad contact but may well be an unrecognized link from<o:p></o:p></span></p>
<p class="MsoNormal" style="background:white"><span style="font-size:8.5pt;font-family:Menlo;color:black;mso-fareast-language:EN-GB"> protein to HETATM residue? It is possible restraints have not been<o:p></o:p></span></p>
<p class="MsoNormal" style="background:white"><span style="font-size:8.5pt;font-family:Menlo;color:black;mso-fareast-language:EN-GB"> properly set up.<o:p></o:p></span></p>
<p class="MsoNormal" style="background:white"><span style="font-size:8.5pt;font-family:Menlo;color:black;mso-fareast-language:EN-GB"> If you want BUSTER to regard this as a bond try adding the<o:p></o:p></span></p>
<p class="MsoNormal" style="background:white"><span style="font-size:8.5pt;font-family:Menlo;color:black;mso-fareast-language:EN-GB"> following card before the CRYST1 line in the input pdb file:<o:p></o:p></span></p>
<p class="MsoNormal" style="background:white"><span style="font-size:8.5pt;font-family:Menlo;color:black;mso-fareast-language:EN-GB"> LINK OH ATYR B 121 C7 LIG E 2 1555 1555 1.68 <o:p></o:p></span></p>
<p class="MsoNormal" style="background:white"><span style="font-size:8.5pt;font-family:Menlo;color:black;mso-fareast-language:EN-GB"> <o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;color:black;mso-fareast-language:EN-GB">Can you point me to the relevant part of the manual or explain how I should set this up?</span><span style="color:black;mso-fareast-language:EN-GB"><o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;color:black;mso-fareast-language:EN-GB"> </span><span style="color:black;mso-fareast-language:EN-GB"><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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