Hi Daron,
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:

1) open some model
2) start Dock Prep, and with the "Add hydrogens" box checked click "OK"
3) ignore the add-hydrogens dialog that comes up as a result
4) close all models
5) open a new model
6) click okay on the add-hydrogen dialog (optionally preceded by selecting Tools->Structure Editing-> AddH)

whereas if I choose "Close" in the add-hydrogens dialog in step (3), I don't get an error.

Does this sound like what you were doing?

--Eric

                        Eric Pettersen
                        UCSF Computer Graphics Lab
                        http://www.cgl.ucsf.edu

On Apr 19, 2011, at 4:09 PM, Daron Standley wrote:

Hi-

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.


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.

So, I then tried preparing the molecules in Chimera. My procedure was:

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.

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'.

3. Save each molecule as an individual pdb file (e.g., 2xnz-G-1.pdb for the first GMP)

4. Read one of the newly created pdb files into chimera

5. run Tools->Structure Editing-> AddH

In either case (with or without step 2) I get the error below.  I have attached both pdb files (bug.zip) for reference.



####################### Error Log #######################

Error in ':ALA': underlying C++ Selectable object is missing
Traceback (most recent call last):
 File "/Applications/Chimera.app/Contents/Resources/lib/python2.7/site-packages/Pmw/Pmw_1_3/lib/PmwBase.py", line 1747, in __call__
   return apply(self.func, args)
 File "/Applications/Chimera.app/Contents/Resources/share/chimera/baseDialog.py", line 346, in command
   getattr(s, buttonFuncName(txt))()
 File "/Applications/Chimera.app/Contents/Resources/share/chimera/baseDialog.py", line 564, in OK
   self.Apply()
 File "/Applications/Chimera.app/Contents/Resources/share/AddH/gui.py", line 265, in Apply
   hisScheme=hisScheme, okCB=self.cb)
 File "/Applications/Chimera.app/Contents/Resources/share/AddH/unknownsGUI.py", line 272, in initiateAddHyd
   okCB()
 File "/Applications/Chimera.app/Contents/Resources/share/DockPrep/__init__.py", line 194, in <lambda>
   cb=lambda pap=_postAddPrep, mols=mols, kw=kw: pap(mols, **kw))
 File "/Applications/Chimera.app/Contents/Resources/share/DockPrep/__init__.py", line 259, in _postAddPrep
   method=method, cb=lambda ur, uc, m=mols, kw=kw:
 File "/Applications/Chimera.app/Contents/Resources/share/AddCharge/__init__.py", line 117, in initiateAddCharges
   chargeModel=chargeModel, nogui=nogui, showCharges=labelStandard)
 File "/Applications/Chimera.app/Contents/Resources/share/AddCharge/__init__.py", line 199, in addStandardCharges
   for r in m.residues:
ValueError: underlying C++ Molecule object is missing
ValueError: underlying C++ Molecule object is missing

 File "/Applications/Chimera.app/Contents/Resources/share/AddCharge/__init__.py", line 199, in addStandardCharges
   for r in m.residues:

See reply log for Python traceback.

####################### End Error Log #######################

Best regards,

Daron


<bug.zip>

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