[Chimera-users] dock prep error in chimera

[Daron Standley]

Hi Eric,

Thanks for your quick reply. You are absolutely right. I can not reproduce the error unless I first open a structure
and ignore the add-hydrogens dialog.  If I just open a new structure and use AddH or Dock Prep, it works!

Looks like it was my error, not Chimeras.

Thanks and sorry for the trouble.

Daron

On Apr 21, 2011, at 5:02 AM, Eric Pettersen wrote:

> 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>
>> 
>> _______________________________________________
>> Chimera-users mailing list
>> Chimera-users at cgl.ucsf.edu
>> http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users
> 
> 
> 
> 
> 

-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://plato.cgl.ucsf.edu/pipermail/chimera-users/attachments/20110421/2a6d3524/attachment.html>