<html><head><meta http-equiv="Content-Type" content="text/html charset=us-ascii"></head><body style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space; ">Hi all,<div>I want to analyze a whole bunch of structures with molprobity, and I am looking for a convenient way to do this.</div><div><br></div><div>phenix.quick_clashlist seems to be a handy tool. However, when I use the following command line:</div><div> "phenix.quick_clashlist model=mypdb.pdb"<br><div apple-content-edited="true">
<span class="Apple-style-span" style="border-collapse: separate; orphans: 2; text-indent: 0px; widows: 2; border-spacing: 0px; "><span class="Apple-style-span" style="border-collapse: separate; orphans: 2; text-indent: 0px; widows: 2; border-spacing: 0px; "><div style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space; "><div style="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-transform: none; white-space: normal; word-spacing: 0px; -webkit-text-decorations-in-effect: none; -webkit-text-size-adjust: auto; -webkit-text-stroke-width: 0px; ">... the output tells me:</div><div><div><font face="Courier New"># run_clashlist</font></div><div><font face="Courier New">#</font></div><div><font face="Courier New"># Run reduce and molprobity </font></div><div><font face="Courier New"># type phenix.run_clashlist: --help for help</font></div><div><font face="Courier New">Parameters used:</font></div><div><font face="Courier New">run_clashlist {</font></div><div><font face="Courier New"> model = "4iuj.pdb"</font></div><div><font face="Courier New"> build = True</font></div><div><font face="Courier New"> summary_file = None</font></div><div><font face="Courier New"> output_file = None</font></div><div><font face="Courier New"> temp_dir = None</font></div><div><font face="Courier New"> remove_temp_dir = None</font></div><div><font face="Courier New"> verbose = False</font></div><div><font face="Courier New"> raise_sorry = False</font></div><div><font face="Courier New"> debug = False</font></div><div><font face="Courier New"> dry_run = True</font></div><div><font face="Courier New">}</font></div><div><font face="Courier New"><br></font></div><div><font face="Courier New"><br></font></div><div><font face="Courier New">************************************************</font></div><div><font face="Courier New">'str' object has no attribute '_anchor'</font></div><div><font face="Courier New"><br></font></div><div><font face="Courier New">************************************************</font></div></div><div style="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-transform: none; white-space: normal; word-spacing: 0px; -webkit-text-decorations-in-effect: none; -webkit-text-size-adjust: auto; -webkit-text-stroke-width: 0px; ">Any ideas what I need to do differently?</div><div style="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-transform: none; white-space: normal; word-spacing: 0px; -webkit-text-decorations-in-effect: none; -webkit-text-size-adjust: auto; -webkit-text-stroke-width: 0px; "><br></div><div style="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-transform: none; white-space: normal; word-spacing: 0px; -webkit-text-decorations-in-effect: none; -webkit-text-size-adjust: auto; -webkit-text-stroke-width: 0px; ">thanks,</div><div style="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-transform: none; white-space: normal; word-spacing: 0px; -webkit-text-decorations-in-effect: none; -webkit-text-size-adjust: auto; -webkit-text-stroke-width: 0px; ">Jan</div><div style="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-transform: none; white-space: normal; word-spacing: 0px; -webkit-text-decorations-in-effect: none; -webkit-text-size-adjust: auto; -webkit-text-stroke-width: 0px; ">--</div><div style="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-transform: none; white-space: normal; word-spacing: 0px; -webkit-text-decorations-in-effect: none; -webkit-text-size-adjust: auto; -webkit-text-stroke-width: 0px; ">Jan Abendroth</div><div style="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-transform: none; white-space: normal; word-spacing: 0px; -webkit-text-decorations-in-effect: none; -webkit-text-size-adjust: auto; -webkit-text-stroke-width: 0px; ">Emerald BioStructures</div><div style="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-transform: none; white-space: normal; word-spacing: 0px; -webkit-text-decorations-in-effect: none; -webkit-text-size-adjust: auto; -webkit-text-stroke-width: 0px; ">Seattle / Bainbridge Island WA, USA</div><div style="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-transform: none; white-space: normal; word-spacing: 0px; -webkit-text-decorations-in-effect: none; -webkit-text-size-adjust: auto; -webkit-text-stroke-width: 0px; "><div>home: Jan.Abendroth_at_gmail.com</div><div>work: JAbendroth_at_embios.com</div><div><a href="http://www.emeraldbiostructures.com">http://www.emeraldbiostructures.com</a></div></div></div></span></span>
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