<html><head></head><body style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space; ">Hi Eric,<div><br></div><div>Thanks for your quick reply. You are absolutely right. I can not reproduce the error unless I first open a structure</div><div>and ignore the add-hydrogens dialog. If I just open a new structure and use AddH or Dock Prep, it works!</div><div><br></div><div>Looks like it was my error, not Chimeras.</div><div><br></div><div>Thanks and sorry for the trouble.</div><div><br></div><div>Daron</div><div><br><div><div>On Apr 21, 2011, at 5:02 AM, Eric Pettersen wrote:</div><br class="Apple-interchange-newline"><blockquote type="cite"><div style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space; ">Hi Daron,<div><span class="Apple-tab-span" style="white-space:pre"> </span>I find that I cannot reproduce your problem with the steps below. However, after looking over the backtrace you provided I was able to determine that I can get the same backtrace if I do this:</div><div><br></div><div>1) open some model</div><div>2) start Dock Prep, and with the "Add hydrogens" box checked click "OK"</div><div>3) ignore the add-hydrogens dialog that comes up as a result</div><div>4) close all models</div><div>5) open a new model</div><div>6) click okay on the add-hydrogen dialog (optionally preceded by selecting Tools->Structure Editing-> AddH)</div><div><br></div><div>whereas if I choose "Close" in the add-hydrogens dialog in step (3), I don't get an error.</div><div><br></div><div>Does this sound like what you were doing?</div><div><br></div><div>--Eric</div><div><br></div><div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; font-size: 16px; "><font face="Helvetica" size="5" style="font: normal normal normal 16px/normal Helvetica; "> Eric Pettersen</font></div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; font-size: 16px; "><font face="Helvetica" size="5" style="font: normal normal normal 16px/normal Helvetica; "> UCSF Computer Graphics Lab</font></div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; font-size: 16px; "><font face="Helvetica" size="5" style="font: normal normal normal 16px/normal Helvetica; "> <a href="http://www.cgl.ucsf.edu/">http://www.cgl.ucsf.edu</a></font></div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; font-size: 16px; "><font face="Helvetica" size="5" style="font: normal normal normal 16px/normal Helvetica; "><br></font></div><div><div>On Apr 19, 2011, at 4:09 PM, Daron Standley wrote:</div><br class="Apple-interchange-newline"><blockquote type="cite"><div>Hi-<br><br>I just submitted the following bug report to chimera. Sorry if this is a redundant report, but I thought perhaps an experienced chimera user could identify my problem, since I am new to using this tool.<br><br><br>I am trying to prepare a ligand for docking. I want to prepare the 4 ribonucleotide monophosphates AMP, GMP, UMP, and CMP. First, I tried extracting these from the Zinc database, but I kept getting related but not quite correct molecules.<br><br>So, I then tried preparing the molecules in Chimera. My procedure was:<br><br>1. Chop up an RNA molecule from the PDB (e.g., 2xnz.pdb) into 'residues' (that is, a single ribonucleotide monophosphate) using a simple perl script.<br><br>2. Optional step 2 (I tried both with and without this step): add an oxygen fromt the previous residue to the phosphate and name it ' OP3'.<br><br>3. Save each molecule as an individual pdb file (e.g., 2xnz-G-1.pdb for the first GMP)<br><br>4. Read one of the newly created pdb files into chimera<br><br>5. run Tools->Structure Editing-> AddH<br><br>In either case (with or without step 2) I get the error below. I have attached both pdb files (bug.zip) for reference.<br><br><br><br>####################### Error Log #######################<br><br>Error in ':ALA': underlying C++ Selectable object is missing<br>Traceback (most recent call last):<br> File "/Applications/Chimera.app/Contents/Resources/lib/python2.7/site-packages/Pmw/Pmw_1_3/lib/PmwBase.py", line 1747, in __call__<br> return apply(self.func, args)<br> File "/Applications/Chimera.app/Contents/Resources/share/chimera/baseDialog.py", line 346, in command<br> getattr(s, buttonFuncName(txt))()<br> File "/Applications/Chimera.app/Contents/Resources/share/chimera/baseDialog.py", line 564, in OK<br> self.Apply()<br> File "/Applications/Chimera.app/Contents/Resources/share/AddH/gui.py", line 265, in Apply<br> hisScheme=hisScheme, okCB=self.cb)<br> File "/Applications/Chimera.app/Contents/Resources/share/AddH/unknownsGUI.py", line 272, in initiateAddHyd<br> okCB()<br> File "/Applications/Chimera.app/Contents/Resources/share/DockPrep/__init__.py", line 194, in <lambda><br> cb=lambda pap=_postAddPrep, mols=mols, kw=kw: pap(mols, **kw))<br> File "/Applications/Chimera.app/Contents/Resources/share/DockPrep/__init__.py", line 259, in _postAddPrep<br> method=method, cb=lambda ur, uc, m=mols, kw=kw:<br> File "/Applications/Chimera.app/Contents/Resources/share/AddCharge/__init__.py", line 117, in initiateAddCharges<br> chargeModel=chargeModel, nogui=nogui, showCharges=labelStandard)<br> File "/Applications/Chimera.app/Contents/Resources/share/AddCharge/__init__.py", line 199, in addStandardCharges<br> for r in m.residues:<br>ValueError: underlying C++ Molecule object is missing<br>ValueError: underlying C++ Molecule object is missing<br><br> File "/Applications/Chimera.app/Contents/Resources/share/AddCharge/__init__.py", line 199, in addStandardCharges<br> for r in m.residues:<br><br>See reply log for Python traceback.<br><br>####################### End Error Log #######################<br><br>Best regards,<br><br>Daron<br><br><br><span><bug.zip></span><br><br>_______________________________________________<br>Chimera-users mailing list<br><a href="mailto:Chimera-users@cgl.ucsf.edu">Chimera-users@cgl.ucsf.edu</a><br><a href="http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users">http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users</a><br></div></blockquote></div><br></div><br><div apple-content-edited="true"><span class="Apple-style-span" style="border-collapse: separate; -webkit-border-horizontal-spacing: 0px; -webkit-border-vertical-spacing: 0px; font-family: Helvetica; font-size: 16px; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: normal; -webkit-text-decorations-in-effect: none; text-indent: 0px; -webkit-text-size-adjust: auto; text-transform: none; orphans: 2; white-space: normal; widows: 2; word-spacing: 0px; "><div style="word-wrap: break-word; -khtml-nbsp-mode: space; -khtml-line-break: after-white-space; "><span class="Apple-style-span" style="font-size: medium;"><br></span><br class="Apple-interchange-newline"></div></span> </div><br></div></blockquote></div><br></div></body></html>