[Chimera-users] dock prep error in chimera

[Eric Pettersen]

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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