<html><head></head><body style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space; "><div>I'm having issues defining planarity restraints in a .edits file. When all four of the atoms in the plane are selected in a single planarity entry, refinement crashes. When I define a single atom in separate planarity restraint entries (as suggested by Nat), refinement doesn't crash, but the four atoms in the plane are treated as four one-atom planes (obviously useless). My previous correspondence is attached below.</div><div><br></div><div>Thanks,</div><div><br></div><div>Elwood</div><div><br></div><div><div style="font-size: 12px; ">=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=</div><div style="font-size: 12px; ">Elwood A. Mullins</div><div style="font-size: 12px; "><span class="Apple-tab-span" style="white-space: pre; "><span class="Apple-style-span" style="white-space: normal; ">Research Associate</span></span></div><div style="font-size: 12px; ">Department of Biochemistry</div><div style="font-size: 12px; ">Purdue University</div><div style="font-size: 12px; ">175 South University Street</div><div style="font-size: 12px; ">West Lafayette, IN 47907-1612</div><div style="font-size: 12px; "><br></div><div style="font-size: 12px; ">Office: Biochemistry 29</div><div style="font-size: 12px; ">Email: <a href="mailto:mullins@purdue.edu">mullins@purdue.edu</a></div><div style="font-size: 12px; ">Tel: (765) 496-6814</div><div style="font-size: 12px; ">Fax: (765) 494-7897</div><div style="font-size: 12px; ">=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=</div></div><div style="font-size: 12px; "><br></div>While refinement didn't crash, I'm not sure this worked. The .geo file lists the desired one plane with four atoms as four planes with one atom and rmsds = 0 with residuals = 0. It also seems impossible to define multiple planes in a .edits file with this syntax. The .geo and the .eff files are attached. I used the .edits file you sent me without modification.<div><br></div><div><div><div><div style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space; "><span class="Apple-style-span" style="border-collapse: separate; color: rgb(0, 0, 0); font-family: Helvetica; font-size: medium; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: normal; orphans: 2; text-indent: 0px; text-transform: none; white-space: normal; widows: 2; word-spacing: 0px; -webkit-border-horizontal-spacing: 0px; -webkit-border-vertical-spacing: 0px; -webkit-text-decorations-in-effect: none; -webkit-text-size-adjust: auto; -webkit-text-stroke-width: 0px; "><div style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space; "><span class="Apple-style-span" style="border-collapse: separate; color: rgb(0, 0, 0); font-family: Helvetica; font-size: medium; font-style: normal; font-variant: normal; font-weight: normal; 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-webkit-border-horizontal-spacing: 0px; -webkit-border-vertical-spacing: 0px; -webkit-text-decorations-in-effect: none; -webkit-text-size-adjust: auto; -webkit-text-stroke-width: 0px; "><div style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space; "><span class="Apple-style-span" style="border-collapse: separate; color: rgb(0, 0, 0); font-family: Helvetica; font-size: medium; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: normal; orphans: 2; text-indent: 0px; text-transform: none; white-space: normal; widows: 2; word-spacing: 0px; -webkit-border-horizontal-spacing: 0px; -webkit-border-vertical-spacing: 0px; -webkit-text-decorations-in-effect: none; -webkit-text-size-adjust: auto; -webkit-text-stroke-width: 0px; "><div style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space; "><span class="Apple-style-span" style="border-collapse: separate; color: rgb(0, 0, 0); font-family: Helvetica; font-size: 12px; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: normal; orphans: 2; text-indent: 0px; text-transform: none; white-space: normal; widows: 2; word-spacing: 0px; -webkit-border-horizontal-spacing: 0px; -webkit-border-vertical-spacing: 0px; -webkit-text-decorations-in-effect: none; -webkit-text-size-adjust: auto; -webkit-text-stroke-width: 0px; "><span class="Apple-style-span" style="border-collapse: separate; color: rgb(0, 0, 0); font-family: Helvetica; font-size: 12px; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: normal; orphans: 2; text-indent: 0px; text-transform: none; white-space: normal; widows: 2; word-spacing: 0px; -webkit-border-horizontal-spacing: 0px; -webkit-border-vertical-spacing: 0px; -webkit-text-decorations-in-effect: none; -webkit-text-size-adjust: auto; -webkit-text-stroke-width: 0px; "><span class="Apple-style-span" style="border-collapse: separate; color: rgb(0, 0, 0); font-family: Helvetica; font-size: 12px; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: normal; orphans: 2; text-indent: 0px; text-transform: none; white-space: normal; widows: 2; word-spacing: 0px; -webkit-border-horizontal-spacing: 0px; -webkit-border-vertical-spacing: 0px; -webkit-text-decorations-in-effect: none; -webkit-text-size-adjust: auto; -webkit-text-stroke-width: 0px; "><span class="Apple-style-span" style="border-collapse: separate; color: rgb(0, 0, 0); font-family: Helvetica; font-size: 12px; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: normal; orphans: 2; text-indent: 0px; text-transform: none; white-space: normal; widows: 2; word-spacing: 0px; -webkit-border-horizontal-spacing: 0px; -webkit-border-vertical-spacing: 0px; -webkit-text-decorations-in-effect: none; -webkit-text-size-adjust: auto; -webkit-text-stroke-width: 0px; "><span class="Apple-style-span" style="border-collapse: separate; color: rgb(0, 0, 0); font-family: Helvetica; font-size: 12px; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: normal; orphans: 2; text-indent: 0px; text-transform: none; white-space: normal; widows: 2; word-spacing: 0px; -webkit-border-horizontal-spacing: 0px; -webkit-border-vertical-spacing: 0px; -webkit-text-decorations-in-effect: none; -webkit-text-size-adjust: auto; -webkit-text-stroke-width: 0px; "><span class="Apple-style-span" style="border-collapse: separate; color: rgb(0, 0, 0); font-family: Helvetica; font-size: 12px; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: normal; orphans: 2; text-indent: 0px; text-transform: none; white-space: normal; widows: 2; word-spacing: 0px; -webkit-border-horizontal-spacing: 0px; -webkit-border-vertical-spacing: 0px; -webkit-text-decorations-in-effect: none; -webkit-text-size-adjust: auto; -webkit-text-stroke-width: 0px; "><span class="Apple-style-span" style="border-collapse: separate; color: rgb(0, 0, 0); font-family: Helvetica; font-size: 12px; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: normal; orphans: 2; text-indent: 0px; text-transform: none; white-space: normal; widows: 2; word-spacing: 0px; -webkit-border-horizontal-spacing: 0px; -webkit-border-vertical-spacing: 0px; -webkit-text-decorations-in-effect: none; -webkit-text-size-adjust: auto; -webkit-text-stroke-width: 0px; "><span class="Apple-style-span" style="border-collapse: separate; color: rgb(0, 0, 0); font-family: Helvetica; font-size: 12px; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: normal; orphans: 2; text-indent: 0px; text-transform: none; white-space: normal; widows: 2; word-spacing: 0px; -webkit-border-horizontal-spacing: 0px; -webkit-border-vertical-spacing: 0px; -webkit-text-decorations-in-effect: none; -webkit-text-size-adjust: auto; -webkit-text-stroke-width: 0px; "><div><div style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space; "><div>=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=</div><div>Elwood A. Mullins</div><div><span class="Apple-tab-span" style="white-space: pre; "><span class="Apple-style-span" style="white-space: normal; ">Research Associate</span></span></div><div>Department of Biochemistry</div><div>Purdue University</div><div>175 South University Street</div><div>West Lafayette, IN 47907-1612</div><div><br></div><div>Office: Biochemistry 29</div><div>Email: <a href="mailto:mullins@purdue.edu">mullins@purdue.edu</a></div><div>Tel: (765) 496-6814</div><div>Fax: (765) 494-7897</div><div>=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=</div></div></div></span></span></span></span></span></span></span></span></div></span></div></span></div></span></div></span></div></span></div></span></div></div><br><div><div>On Jul 22, 2010, at 2:45 PM, Nathaniel Echols wrote:</div><br class="Apple-interchange-newline"><blockquote type="cite">On Thu, Jul 22, 2010 at 2:41 PM, Elwood A. Mullins <span dir="ltr"><<a href="mailto:mullins@purdue.edu">mullins@purdue.edu</a>></span> wrote:<br><div class="gmail_quote"><blockquote class="gmail_quote" style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0.8ex; border-left-width: 1px; border-left-color: rgb(204, 204, 204); border-left-style: solid; padding-left: 1ex; "><div style="word-wrap: break-word; ">I'm loading a .edits file. It seems to work fine for the bond and angles. The file is attached.</div></blockquote><div><br></div><div>Okay, it's just a syntax error - only bonds and angles have multiple atom selections (2 and 3, respectively). For planarity, you define each plane separately, and you only need a single atom selection each, for all atoms in the plane. Try the attached file with corrected parameters; let me know if this doesn't fix it.</div><div><br></div><div>thanks,</div><div>Nat</div><div><br></div><blockquote class="gmail_quote" style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0.8ex; border-left-width: 1px; border-left-color: rgb(204, 204, 204); border-left-style: solid; padding-left: 1ex; "><div style="word-wrap: break-word; "><div></div></div><br><div style="word-wrap: break-word; "><div><br><div><div style="word-wrap: break-word; "><span style="border-collapse: separate; color: rgb(0, 0, 0); font-family: Helvetica; font-size: medium; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: normal; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px; "><div style="word-wrap: break-word; "><span style="border-collapse: separate; color: rgb(0, 0, 0); font-family: Helvetica; font-size: medium; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: normal; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px; "><div style="word-wrap: break-word; "><span style="border-collapse: separate; color: rgb(0, 0, 0); font-family: Helvetica; font-size: medium; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: normal; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px; "><div style="word-wrap: break-word; "><span style="border-collapse: separate; color: rgb(0, 0, 0); font-family: Helvetica; font-size: medium; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: normal; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px; "><div style="word-wrap: break-word; "><span style="border-collapse: separate; color: rgb(0, 0, 0); font-family: Helvetica; font-size: medium; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: normal; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px; "><div style="word-wrap: break-word; "><span style="border-collapse: separate; color: rgb(0, 0, 0); font-family: Helvetica; font-size: medium; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: normal; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px; "><div style="word-wrap: break-word; "><span style="border-collapse: separate; color: rgb(0, 0, 0); font-family: Helvetica; font-size: 12px; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: normal; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px; "><span style="border-collapse: separate; color: rgb(0, 0, 0); font-family: Helvetica; font-size: 12px; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: normal; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px; "><span style="border-collapse: separate; color: rgb(0, 0, 0); font-family: Helvetica; font-size: 12px; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: normal; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px; "><span style="border-collapse: separate; color: rgb(0, 0, 0); font-family: Helvetica; font-size: 12px; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: normal; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px; "><span style="border-collapse: separate; color: rgb(0, 0, 0); font-family: Helvetica; font-size: 12px; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: normal; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px; "><span style="border-collapse: separate; color: rgb(0, 0, 0); font-family: Helvetica; font-size: 12px; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: normal; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px; "><span style="border-collapse: separate; color: rgb(0, 0, 0); font-family: Helvetica; font-size: 12px; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: normal; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px; "><span style="border-collapse: separate; color: rgb(0, 0, 0); font-family: Helvetica; font-size: 12px; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: normal; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px; "><div><div style="word-wrap: break-word; "><div>=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=</div><div>Elwood A. Mullins</div><div><span style="white-space: pre-wrap; "><span style="white-space: normal; ">Research Associate</span></span></div><div>Department of Biochemistry</div><div>Purdue University</div><div>175 South University Street</div><div>West Lafayette, IN 47907-1612</div><div><br></div><div>Office: Biochemistry 29</div><div>Email: <a href="mailto:mullins@purdue.edu" target="_blank">mullins@purdue.edu</a></div><div>Tel: (765) 496-6814</div><div>Fax: (765) 494-7897</div><div>=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=</div></div></div></span></span></span></span></span></span></span></span></div></span></div></span></div></span></div></span></div></span></div></span></div></div><br><div><div>On Jul 22, 2010, at 2:20 PM, Nathaniel Echols wrote:</div><br><blockquote type="cite">Sorry, I forgot to read your original message before I sent this. I take it you're loading a .eff file into the GUI? Could you please send me this file?<div><br></div><div>thanks,</div><div>Nat<br><br><div class="gmail_quote">On Thu, Jul 22, 2010 at 2:20 PM, Nathaniel Echols <span dir="ltr"><<a href="mailto:nechols@lbl.gov" target="_blank">nechols@lbl.gov</a>></span> wrote:<br><blockquote class="gmail_quote" style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0.8ex; border-left-width: 1px; border-left-color: rgb(204, 204, 204); border-left-style: solid; padding-left: 1ex; ">The atom selection for the planarity is missing - I suspect this is the problem. What did you enter in the GUI?<br><br><div class="gmail_quote"><div>On Thu, Jul 22, 2010 at 2:18 PM, Elwood A. Mullins <span dir="ltr"><<a href="mailto:mullins@purdue.edu" target="_blank">mullins@purdue.edu</a>></span> wrote:<br></div><blockquote class="gmail_quote" style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0.8ex; border-left-width: 1px; border-left-color: rgb(204, 204, 204); border-left-style: solid; padding-left: 1ex; "><div><div style="word-wrap: break-word; ">I've tried a couple different sigma values (0.02 and 0.1) and received the same error. The .eff file is attached below.<div><br></div><div></div></div><br></div><div style="word-wrap: break-word; "><div><br><div><div style="word-wrap: break-word; "><div style="word-wrap: break-word; "><span style="border-collapse: separate; color: rgb(0, 0, 0); font-family: Helvetica; font-size: medium; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: normal; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px; "><div style="word-wrap: break-word; "><span style="border-collapse: separate; color: rgb(0, 0, 0); font-family: Helvetica; font-size: medium; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: normal; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px; "><div style="word-wrap: break-word; "><span style="border-collapse: separate; color: rgb(0, 0, 0); font-family: Helvetica; font-size: medium; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: normal; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px; "><div style="word-wrap: break-word; "><span style="border-collapse: separate; color: rgb(0, 0, 0); font-family: Helvetica; font-size: medium; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: normal; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px; "><div style="word-wrap: break-word; "><span style="border-collapse: separate; color: rgb(0, 0, 0); font-family: Helvetica; font-size: medium; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: normal; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px; "><div style="word-wrap: break-word; "><span style="border-collapse: separate; color: rgb(0, 0, 0); font-family: Helvetica; font-size: 12px; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: normal; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px; "><span style="border-collapse: separate; color: rgb(0, 0, 0); font-family: Helvetica; font-size: 12px; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: normal; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px; "><span style="border-collapse: separate; color: rgb(0, 0, 0); font-family: Helvetica; font-size: 12px; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: normal; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px; "><span style="border-collapse: separate; color: rgb(0, 0, 0); font-family: Helvetica; font-size: 12px; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: normal; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px; "><span style="border-collapse: separate; color: rgb(0, 0, 0); font-family: Helvetica; font-size: 12px; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: normal; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px; "><span style="border-collapse: separate; color: rgb(0, 0, 0); font-family: Helvetica; font-size: 12px; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: normal; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px; "><span style="border-collapse: separate; color: rgb(0, 0, 0); font-family: Helvetica; font-size: 12px; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: normal; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px; "><span style="border-collapse: separate; color: rgb(0, 0, 0); font-family: Helvetica; font-size: 12px; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: normal; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px; "><div><div style="word-wrap: break-word; "><div>=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=</div><div>Elwood A. Mullins</div><div><span style="white-space: pre-wrap; "><span style="white-space: normal; ">Research Associate</span></span></div><div>Department of Biochemistry</div><div>Purdue University</div><div>175 South University Street</div><div>West Lafayette, IN 47907-1612</div><div><br></div><div>Office: Biochemistry 29</div><div>Email: <a href="mailto:mullins@purdue.edu" target="_blank">mullins@purdue.edu</a></div><div>Tel: (765) 496-6814</div><div>Fax: (765) 494-7897</div><div>=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=</div></div></div></span></span></span></span></span></span></span></span></div></span></div></span></div></span></div></span></div></span></div></div></div><div><div></div><div><br><div><div>On Jul 22, 2010, at 2:00 PM, Nathaniel Echols wrote:</div><br><blockquote type="cite">Could you please send me the final .eff file written by the GUI? (You can save a copy by clicking the Save button on the toolbar instead of running it.) I suspect the problem is with incorrect sigma values, but it's hard to tell from this error, which is coming from C++ code.<div><br></div><div>thanks,</div><div>Nat<br><br><div class="gmail_quote">---------- Forwarded message ----------<br>From: <b class="gmail_sendername"></b><span dir="ltr"><<a href="mailto:bugs-from-web@phenix-online.org" target="_blank">bugs-from-web@phenix-online.org</a>></span><br>Date: Thu, Jul 22, 2010 at 1:57 PM<br>Subject: <br>To: <br><br><br> User name: Elwood Mullins<br> E-mail address: <a href="mailto:mullins@purdue.edu" target="_blank">mullins@purdue.edu</a><br> Version: 1.6.3-473<br> Platform: mac-intel-osx<br> Comments: This error only occurs when I add planarity restraints to the bond and angle restraints in the restraints.edits file.<br><br> Traceback:<br>RuntimeError : cctbx InternalError: /net/patchnose/scratch1/phenix/phenix-1.6.3-473/cctbx_project/cctbx/geometry_restraints/planarity.h(326): CCTBX_ASSERT(sum_weights > 0) failure.<br>Traceback:<br> File "/usr/local/phenix-1.6.3-473/cctbx_project/libtbx/thread_utils.py", line 141, in run<br> return_value = self._target(self._args, self._kwargs, self._c)<br><br> File "/usr/local/phenix-1.6.3-473/cctbx_project/libtbx/runtime_utils.py", line 58, in __call__<br> result = self.target()<br><br> File "/usr/local/phenix-1.6.3-473/phenix/phenix/refinement/runtime.py", line 35, in __call__<br> call_back_handler=callback)<br><br> File "/usr/local/phenix-1.6.3-473/phenix/phenix/refinement/command_line.py", line 71, in run<br> overwrite = command_line_interpreter.command_line.options.overwrite)<br><br> File "/usr/local/phenix-1.6.3-473/phenix/phenix/refinement/driver.py", line 132, in __init__<br> assume_hydrogens_all_missing = not has_hd)<br><br> File "/usr/local/phenix-1.6.3-473/cctbx_project/mmtbx/monomer_library/pdb_interpretation.py", line 3490, in geometry_restraints_manager<br> log=self.log)<br><br> File "/usr/local/phenix-1.6.3-473/cctbx_project/mmtbx/monomer_library/pdb_interpretation.py", line 3243, in construct_geometry_restraints_manager<br> params=params_edits, log=log)<br><br> File "/usr/local/phenix-1.6.3-473/cctbx_project/mmtbx/monomer_library/pdb_interpretation.py", line 3080, in process_geometry_restraints_edits<br> sel_cache=sel_cache, params=params, log=log)<br><br> File "/usr/local/phenix-1.6.3-473/cctbx_project/mmtbx/monomer_library/pdb_interpretation.py", line 3068, in process_geometry_restraints_edits_planarity<br> proxy=proxy)<br><br><br><br> Platform info:<br> __FILE__ = /net/patchnose/scratch1/phenix/phenix-1.6.3-473/cctbx_project/boost_adaptbx/meta_ext.cpp<br>__DATE__ = Jul 18 2010<br>__TIME__ = 03:42:23<br>__i386__<br>__APPLE_CC__ = 5367<br>__GNUC__ = 4<br>__GNUC_MINOR__ = 0<br>__GNUC_PATCHLEVEL__ = 1<br>boost::python::cxxabi_cxa_demangle_is_broken(): false<br>__GXX_WEAK__ = 1<br>__VERSION__ = 4.0.1 (Apple Computer, Inc. build 5367)<br>FE_INEXACT = 32<br>FE_DIVBYZERO = 4<br>FE_UNDERFLOW = 16<br>FE_OVERFLOW = 8<br>FE_INVALID = 1<br>FE_ALL_EXCEPT = 61<br>__SSE2__ = 1<br>PY_VERSION = 2.6.5<br>PYTHON_API_VERSION = 1013<br>sizeof(bool) = 1<br>sizeof(short) = 2<br>sizeof(int) = 4<br>sizeof(long) = 4<br>sizeof(std::size_t) = 4<br>sizeof(void*) = 4<br>sizeof(long long) = 8<br>sizeof(float) = 4<br>sizeof(double) = 8<br>sizeof(long double) = 16<br>sizeof(boost::int32_t) = 4<br>sizeof(boost::uint32_t) = 4<br>sizeof(wchar_t) = 4<br>__PTRDIFF_TYPE__<br>Py_USING_UNICODE<br>sizeof(PY_UNICODE_TYPE) = 2<br>BOOST_ADAPTBX_TYPE_ID_SIZE_T_EQ_UNSIGNED_LONG<br><a href="http://os.name/" target="_blank">os.name</a>: posix<br>sys.platform: darwin<br>sys.byteorder: little<br>platform.platform(): Darwin-10.4.0-i386-32bit<br>platform.architecture(): ('32bit', '')<br>floating_point_exceptions.division_by_zero_trapped: False<br>floating_point_exceptions.invalid_trapped: False<br>floating_point_exceptions.overflow_trapped: False<br>number of processors: 2<br>Memory total: 4,294,967,296<br>Memory free: unknown<br>import thread: OK<br>"hello" = ['h', 'e', 'l', 'l', 'o']<br>u"hello" = ['h', '\x00', 'e', '\x00', 'l', '\x00', 'l', '\x00', 'o', '\x00']<br>u"\u00C5" = ['\xc5', '\x00'] as utf-8 = ['\xc3', '\x85']<br>LATIN CAPITAL LETTER A WITH RING ABOVE = �<br><br><br></div><br></div></blockquote></div><br></div></div></div></div><br></blockquote></div><br></blockquote></div><br></div></blockquote></div><br></div></div><br></blockquote></div><br><span><refinement.geometry_restraints.edits></span></blockquote></div></div></div><div><span><br></span></div><div>
<span class="Apple-style-span" style="border-collapse: separate; color: rgb(0, 0, 0); font-family: Helvetica; font-size: medium; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: normal; orphans: 2; text-align: auto; text-indent: 0px; text-transform: none; white-space: normal; widows: 2; word-spacing: 0px; -webkit-border-horizontal-spacing: 0px; -webkit-border-vertical-spacing: 0px; -webkit-text-decorations-in-effect: none; -webkit-text-size-adjust: auto; -webkit-text-stroke-width: 0px; "><span class="Apple-style-span" style="border-collapse: separate; color: rgb(0, 0, 0); font-family: Helvetica; font-size: medium; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: normal; orphans: 2; text-indent: 0px; text-transform: none; white-space: normal; widows: 2; word-spacing: 0px; -webkit-border-horizontal-spacing: 0px; -webkit-border-vertical-spacing: 0px; -webkit-text-decorations-in-effect: none; -webkit-text-size-adjust: auto; -webkit-text-stroke-width: 0px; "><div style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space; "><span class="Apple-style-span" style="border-collapse: separate; color: rgb(0, 0, 0); font-family: Helvetica; font-size: medium; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: normal; orphans: 2; text-indent: 0px; text-transform: none; white-space: normal; widows: 2; word-spacing: 0px; -webkit-border-horizontal-spacing: 0px; -webkit-border-vertical-spacing: 0px; -webkit-text-decorations-in-effect: none; -webkit-text-size-adjust: auto; -webkit-text-stroke-width: 0px; "><div style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space; "><span class="Apple-style-span" style="border-collapse: separate; color: rgb(0, 0, 0); font-family: Helvetica; font-size: medium; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: normal; orphans: 2; text-indent: 0px; text-transform: none; white-space: normal; widows: 2; word-spacing: 0px; -webkit-border-horizontal-spacing: 0px; -webkit-border-vertical-spacing: 0px; -webkit-text-decorations-in-effect: none; -webkit-text-size-adjust: auto; -webkit-text-stroke-width: 0px; "><div style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space; "><span class="Apple-style-span" style="border-collapse: separate; color: rgb(0, 0, 0); font-family: Helvetica; font-size: medium; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: normal; orphans: 2; text-indent: 0px; text-transform: none; white-space: normal; widows: 2; word-spacing: 0px; -webkit-border-horizontal-spacing: 0px; -webkit-border-vertical-spacing: 0px; -webkit-text-decorations-in-effect: none; -webkit-text-size-adjust: auto; -webkit-text-stroke-width: 0px; "><div style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space; "><span class="Apple-style-span" style="border-collapse: separate; color: rgb(0, 0, 0); font-family: Helvetica; font-size: medium; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: normal; orphans: 2; text-indent: 0px; text-transform: none; white-space: normal; widows: 2; word-spacing: 0px; -webkit-border-horizontal-spacing: 0px; -webkit-border-vertical-spacing: 0px; -webkit-text-decorations-in-effect: none; -webkit-text-size-adjust: auto; -webkit-text-stroke-width: 0px; "><div style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space; "><span class="Apple-style-span" style="border-collapse: separate; color: rgb(0, 0, 0); font-family: Helvetica; font-size: medium; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: normal; orphans: 2; text-indent: 0px; text-transform: none; white-space: normal; widows: 2; word-spacing: 0px; -webkit-border-horizontal-spacing: 0px; -webkit-border-vertical-spacing: 0px; -webkit-text-decorations-in-effect: none; -webkit-text-size-adjust: auto; -webkit-text-stroke-width: 0px; "><div style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space; "><span class="Apple-style-span" style="border-collapse: separate; color: rgb(0, 0, 0); font-family: Helvetica; font-size: medium; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: normal; orphans: 2; text-indent: 0px; text-transform: none; white-space: normal; widows: 2; word-spacing: 0px; -webkit-border-horizontal-spacing: 0px; -webkit-border-vertical-spacing: 0px; -webkit-text-decorations-in-effect: none; -webkit-text-size-adjust: auto; -webkit-text-stroke-width: 0px; "><div style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space; "><span class="Apple-style-span" style="border-collapse: separate; color: rgb(0, 0, 0); font-family: Helvetica; font-size: 12px; 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font-family: Helvetica; font-size: 12px; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: normal; orphans: 2; text-indent: 0px; text-transform: none; white-space: normal; widows: 2; word-spacing: 0px; -webkit-border-horizontal-spacing: 0px; -webkit-border-vertical-spacing: 0px; -webkit-text-decorations-in-effect: none; -webkit-text-size-adjust: auto; -webkit-text-stroke-width: 0px; "><span class="Apple-style-span" style="border-collapse: separate; color: rgb(0, 0, 0); font-family: Helvetica; font-size: 12px; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: normal; orphans: 2; text-indent: 0px; text-transform: none; white-space: normal; widows: 2; word-spacing: 0px; -webkit-border-horizontal-spacing: 0px; -webkit-border-vertical-spacing: 0px; -webkit-text-decorations-in-effect: none; -webkit-text-size-adjust: auto; -webkit-text-stroke-width: 0px; "><span class="Apple-style-span" style="border-collapse: separate; color: rgb(0, 0, 0); font-family: Helvetica; font-size: 12px; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: normal; orphans: 2; text-indent: 0px; text-transform: none; white-space: normal; widows: 2; word-spacing: 0px; -webkit-border-horizontal-spacing: 0px; -webkit-border-vertical-spacing: 0px; -webkit-text-decorations-in-effect: none; -webkit-text-size-adjust: auto; -webkit-text-stroke-width: 0px; "><span class="Apple-style-span" style="border-collapse: separate; color: rgb(0, 0, 0); font-family: Helvetica; font-size: 12px; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: normal; orphans: 2; text-indent: 0px; text-transform: none; white-space: normal; widows: 2; word-spacing: 0px; -webkit-border-horizontal-spacing: 0px; -webkit-border-vertical-spacing: 0px; -webkit-text-decorations-in-effect: none; -webkit-text-size-adjust: auto; -webkit-text-stroke-width: 0px; "><span class="Apple-style-span" style="border-collapse: separate; color: rgb(0, 0, 0); font-family: Helvetica; font-size: 12px; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: normal; orphans: 2; text-indent: 0px; text-transform: none; white-space: normal; widows: 2; word-spacing: 0px; -webkit-border-horizontal-spacing: 0px; -webkit-border-vertical-spacing: 0px; -webkit-text-decorations-in-effect: none; -webkit-text-size-adjust: auto; -webkit-text-stroke-width: 0px; "><span class="Apple-style-span" style="border-collapse: separate; color: rgb(0, 0, 0); font-family: Helvetica; font-size: 12px; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: normal; orphans: 2; text-indent: 0px; text-transform: none; white-space: normal; widows: 2; word-spacing: 0px; -webkit-border-horizontal-spacing: 0px; -webkit-border-vertical-spacing: 0px; -webkit-text-decorations-in-effect: none; -webkit-text-size-adjust: auto; -webkit-text-stroke-width: 0px; "><div><div style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space; "><div>=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=</div><div>Elwood A. Mullins</div><div><span class="Apple-tab-span" style="white-space: pre; "><span class="Apple-style-span" style="white-space: normal; ">Research Associate</span></span></div><div>Department of Biochemistry</div><div>Purdue University</div><div>175 South University Street</div><div>West Lafayette, IN 47907-1612</div><div><br></div><div>Office: Biochemistry 29</div><div>Email: <a href="mailto:mullins@purdue.edu">mullins@purdue.edu</a></div><div>Tel: (765) 496-6814</div><div>Fax: (765) 494-7897</div><div>=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=</div></div></div></span></span></span></span></span></span></span></span></div></span></div></span></div></span></div></span></div></span></div></span></div></span></span>
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<br><div><div>On Jul 21, 2010, at 5:11 PM, Ralf W. Grosse-Kunstleve wrote:</div><br class="Apple-interchange-newline"><blockquote type="cite"><div><blockquote type="cite">I'm trying to refine a thioester linkage (CoA to<br></blockquote><blockquote type="cite">glutamate). Is it possible to define planarity restraints in a<br></blockquote><blockquote type="cite">refinement.geometry_restraints.edits file along with bonds and<br></blockquote><blockquote type="cite">angles?<br></blockquote><br>Yes, this was added recently by Jeff. In the 1.6.3 release<br>you can define custom planarities like this:<br><br>refinement.geometry_restraints.edits {<br> planarity {<br> action = *add delete change<br> atom_selection = chain A and resid 123 and (name C or name N or name O)<br> sigma = 0.02<br> }<br>}<br><br>Ralf<br>_______________________________________________<br>phenixbb mailing list<br><a href="mailto:phenixbb@phenix-online.org">phenixbb@phenix-online.org</a><br>http://phenix-online.org/mailman/listinfo/phenixbb<br></div></blockquote></div><br></body></html>