<div dir="ltr">Hi Pascal,<div><br></div><div>I apologize for the delayed reply. Thank you for bringing this to our attention.</div><div><br></div><div>Regarding GUI, can you please change the extension of the file to just ".params" instead of ".params.cif"? This "cif" ending may confuse the GUI.</div><div><br></div><div>Given that there is no way to have residue id > 9999 in PDB format I assume you are using mmCIF and get something like </div><div><br></div><div><font face="monospace"> Custom bonds:<br>Sorry: No atom selected: "chain 0 and resname HOH and resid 13322 and name O"<br></font></div><div><br></div><div>when you try to use your parameters in the command line.</div><div><br></div><div>We will work on fixing this issue in the near future. </div><div><br></div><div>Meanwhile:</div><div><br></div><div>For resids and atom numbers > 9999 Phenix uses hybrid 36 encoding:</div><div><a href="http://cci.lbl.gov/hybrid_36/">http://cci.lbl.gov/hybrid_36/</a><br></div><div><a href="https://github.com/cctbx/cctbx_project/blob/master/iotbx/pdb/hybrid_36.py">https://github.com/cctbx/cctbx_project/blob/master/iotbx/pdb/hybrid_36.py</a><br></div><div><br></div><div>Therefore you can try to use this encoding in your parameter file. For example, "resid 13322" will translate to "resid A2KA". </div><div>There are several ways to figure out this encoding:</div><div><br></div><div>1. Run phenix.cif_as_pdb <your model.cif> and get PDB file where resids will be encoded with hybrid36.</div><div><br></div><div>2. if you have python with cctbx library:<br><span style="font-family:monospace"> from iotbx.pdb.hybrid_36 import hy36encode</span><br></div><div><font face="monospace"> hy36encode(width=4, value=13322)</font></div><div><font face="monospace"><br></font></div><div><font face="arial, sans-serif">Other option would be splitting chain with > 10k residues into several chains with less than 10k residues.</font></div><div><font face="arial, sans-serif"><br></font></div><div><font face="arial, sans-serif">Best regards,</font></div><div><font face="arial, sans-serif">Oleg Sobolev.</font></div></div><br><div class="gmail_quote"><div dir="ltr" class="gmail_attr">On Thu, Mar 23, 2023 at 1:26 PM p.auffinger <<a href="mailto:p.auffinger@unistra.fr">p.auffinger@unistra.fr</a>> wrote:<br></div><blockquote class="gmail_quote" style="margin:0px 0px 0px 0.8ex;border-left:1px solid rgb(204,204,204);padding-left:1ex"><div style="overflow-wrap: break-word;"><div><div style="color:rgb(0,0,0);font-family:Helvetica;font-size:14px;font-style:normal;font-variant-caps:normal;font-weight:normal;letter-spacing:normal;text-align:start;text-indent:0px;text-transform:none;white-space:normal;word-spacing:0px;text-decoration:none">Hi phenix users,</div><div style="color:rgb(0,0,0);font-family:Helvetica;font-size:14px;font-style:normal;font-variant-caps:normal;font-weight:normal;letter-spacing:normal;text-align:start;text-indent:0px;text-transform:none;white-space:normal;word-spacing:0px;text-decoration:none"><br></div><div style="color:rgb(0,0,0);font-family:Helvetica;font-size:14px;font-style:normal;font-variant-caps:normal;font-weight:normal;letter-spacing:normal;text-align:start;text-indent:0px;text-transform:none;white-space:normal;word-spacing:0px;text-decoration:none">I started to add restraints to a large ribosomal file</div><div style="color:rgb(0,0,0);font-family:Helvetica;font-size:14px;font-style:normal;font-variant-caps:normal;font-weight:normal;letter-spacing:normal;text-align:start;text-indent:0px;text-transform:none;white-space:normal;word-spacing:0px;text-decoration:none">by using the file (in full) below.</div><div style="color:rgb(0,0,0);font-family:Helvetica;font-size:14px;font-style:normal;font-variant-caps:normal;font-weight:normal;letter-spacing:normal;text-align:start;text-indent:0px;text-transform:none;white-space:normal;word-spacing:0px;text-decoration:none"><br></div><div style="color:rgb(0,0,0);font-family:Helvetica;font-size:14px;font-style:normal;font-variant-caps:normal;font-weight:normal;letter-spacing:normal;text-align:start;text-indent:0px;text-transform:none;white-space:normal;word-spacing:0px;text-decoration:none">I encountered two issues:</div><div style="color:rgb(0,0,0);font-family:Helvetica;font-size:14px;font-style:normal;font-variant-caps:normal;font-weight:normal;letter-spacing:normal;text-align:start;text-indent:0px;text-transform:none;white-space:normal;word-spacing:0px;text-decoration:none"><br></div><div style="color:rgb(0,0,0);font-family:Helvetica;font-size:14px;font-style:normal;font-variant-caps:normal;font-weight:normal;letter-spacing:normal;text-align:start;text-indent:0px;text-transform:none;white-space:normal;word-spacing:0px;text-decoration:none">1)</div><div style="color:rgb(0,0,0);font-family:Helvetica;font-size:14px;font-style:normal;font-variant-caps:normal;font-weight:normal;letter-spacing:normal;text-align:start;text-indent:0px;text-transform:none;white-space:normal;word-spacing:0px;text-decoration:none">The first one is:</div><div style="color:rgb(0,0,0);font-family:Helvetica;font-size:14px;font-style:normal;font-variant-caps:normal;font-weight:normal;letter-spacing:normal;text-align:start;text-indent:0px;text-transform:none;white-space:normal;word-spacing:0px;text-decoration:none">how to use this file in the GUI?</div><div style="color:rgb(0,0,0);font-family:Helvetica;font-size:14px;font-style:normal;font-variant-caps:normal;font-weight:normal;letter-spacing:normal;text-align:start;text-indent:0px;text-transform:none;white-space:normal;word-spacing:0px;text-decoration:none">It seems to get rejected while its accepted </div><div style="color:rgb(0,0,0);font-family:Helvetica;font-size:14px;font-style:normal;font-variant-caps:normal;font-weight:normal;letter-spacing:normal;text-align:start;text-indent:0px;text-transform:none;white-space:normal;word-spacing:0px;text-decoration:none">when I run phenix through the command line.</div><div style="color:rgb(0,0,0);font-family:Helvetica;font-size:14px;font-style:normal;font-variant-caps:normal;font-weight:normal;letter-spacing:normal;text-align:start;text-indent:0px;text-transform:none;white-space:normal;word-spacing:0px;text-decoration:none"><br></div><div style="color:rgb(0,0,0);font-family:Helvetica;font-size:14px;font-style:normal;font-variant-caps:normal;font-weight:normal;letter-spacing:normal;text-align:start;text-indent:0px;text-transform:none;white-space:normal;word-spacing:0px;text-decoration:none">2)</div><div style="color:rgb(0,0,0);font-family:Helvetica;font-size:14px;font-style:normal;font-variant-caps:normal;font-weight:normal;letter-spacing:normal;text-align:start;text-indent:0px;text-transform:none;white-space:normal;word-spacing:0px;text-decoration:none">The second is:</div><div style="color:rgb(0,0,0);font-family:Helvetica;font-size:14px;font-style:normal;font-variant-caps:normal;font-weight:normal;letter-spacing:normal;text-align:start;text-indent:0px;text-transform:none;white-space:normal;word-spacing:0px;text-decoration:none">restraints involving water molecules with</div><div style="color:rgb(0,0,0);font-family:Helvetica;font-size:14px;font-style:normal;font-variant-caps:normal;font-weight:normal;letter-spacing:normal;text-align:start;text-indent:0px;text-transform:none;white-space:normal;word-spacing:0px;text-decoration:none">residue numbers > 9999 get rejected.</div><div style="color:rgb(0,0,0);font-family:Helvetica;font-size:14px;font-style:normal;font-variant-caps:normal;font-weight:normal;letter-spacing:normal;text-align:start;text-indent:0px;text-transform:none;white-space:normal;word-spacing:0px;text-decoration:none">Could that limit be overcome through a future</div><div style="color:rgb(0,0,0);font-family:Helvetica;font-size:14px;font-style:normal;font-variant-caps:normal;font-weight:normal;letter-spacing:normal;text-align:start;text-indent:0px;text-transform:none;white-space:normal;word-spacing:0px;text-decoration:none">patch?</div><div style="color:rgb(0,0,0);font-family:Helvetica;font-size:14px;font-style:normal;font-variant-caps:normal;font-weight:normal;letter-spacing:normal;text-align:start;text-indent:0px;text-transform:none;white-space:normal;word-spacing:0px;text-decoration:none"><br></div><div style="color:rgb(0,0,0);font-family:Helvetica;font-size:14px;font-style:normal;font-variant-caps:normal;font-weight:normal;letter-spacing:normal;text-align:start;text-indent:0px;text-transform:none;white-space:normal;word-spacing:0px;text-decoration:none">###</div><div style="text-align:start;text-indent:0px"><div>refinement.geometry_restraints.edits {</div><div> MG_8078 = chain 0 and resname MG and resid 8078 and name MG</div><div> W_12641 = chain 0 and resname HOH and resid 12641 and name O </div><div> bond {</div><div> action = *add</div><div> atom_selection_1 = $MG_8078</div><div> atom_selection_2 = $W_12641</div><div> symmetry_operation = None</div><div> distance_ideal = 2.2</div><div> sigma = 0.1</div><div> slack = None</div><div> }</div><div> }</div><div>###</div><div><br></div><div>Thanks for any thoughts on this,</div><div><br></div><div>Pascal</div></div><div style="color:rgb(0,0,0);font-family:Helvetica;font-size:14px;font-style:normal;font-variant-caps:normal;font-weight:normal;letter-spacing:normal;text-align:start;text-indent:0px;text-transform:none;white-space:normal;word-spacing:0px;text-decoration:none"><br></div><div style="color:rgb(0,0,0);font-family:Helvetica;font-size:14px;font-style:normal;font-variant-caps:normal;font-weight:normal;letter-spacing:normal;text-align:start;text-indent:0px;text-transform:none;white-space:normal;word-spacing:0px;text-decoration:none"></div></div></div><div style="overflow-wrap: break-word;"><div><div style="color:rgb(0,0,0);font-family:Helvetica;font-size:14px;font-style:normal;font-variant-caps:normal;font-weight:normal;letter-spacing:normal;text-align:start;text-indent:0px;text-transform:none;white-space:normal;word-spacing:0px;text-decoration:none"><br><br>-----<br>Pascal Auffinger<br>IBMC/CNRS<br>15 rue René Descartes<br>67084 Strasbourg Cedex<br><br><a href="mailto:p.auffinger@ibmc-cnrs.unistra.fr" target="_blank">p.auffinger@ibmc-cnrs.unistra.fr</a><br>-----</div>
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