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
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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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>
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participants (2)
-
Daron Standley -
Eric Pettersen