Attribute Error: 'AtomType' object has no attribute 'amber_atom_type'
Hi I am modifying several ligand/protein complexes; usually with the “Build Structures” tool. I modify ligands by changing and deleting atoms, or by using “Join Models” after building or importing a structure with “Start structure”. Sometimes, minimizing the ligand works fine, but other times I get the error: “Attribute Error: ‘AtomType’ object has no attribute ‘amber_atom_type’”. I cannot figure out what is causing this error or how to fix it. It seems to happen when I begin working from a saved session or a pdb that was written with the ‘write’ command and not when I go through a whole series of steps in one shot. Any ideas on what is going on? Thanks, All the best, Karl -- Dr Karl Sebby Left Side Research LLC 1661 K M Ranch Road Whitefish Montana 59937 Office: 406 623 4773
Hi Karl, We have not encountered this behavior. Do you have a session or PDB file where this happens reliably for you? If so, could you use Chimera's Help->Report A Bug and attach the file? I can keep the data private if that's an issue. --Eric Eric Pettersen UCSF Computer Graphics Lab http://www.cgl.ucsf.edu On Jun 19, 2015, at 3:32 PM, Karl Sebby <karl.sebby@leftsideresearch.com> wrote:
Hi I am modifying several ligand/protein complexes; usually with the “Build Structures” tool. I modify ligands by changing and deleting atoms, or by using “Join Models” after building or importing a structure with “Start structure”. Sometimes, minimizing the ligand works fine, but other times I get the error: “Attribute Error: ‘AtomType’ object has no attribute ‘amber_atom_type’”. I cannot figure out what is causing this error or how to fix it. It seems to happen when I begin working from a saved session or a pdb that was written with the ‘write’ command and not when I go through a whole series of steps in one shot. Any ideas on what is going on? Thanks, All the best, Karl -- Dr Karl Sebby
Left Side Research LLC 1661 K M Ranch Road Whitefish Montana 59937 Office: 406 623 4773
_______________________________________________ Chimera-users mailing list Chimera-users@cgl.ucsf.edu http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users
Actually, just accidentally noticed a similar reported problem in our bug database. It can happen if you assign non-unique names to atoms in a residue (e.g. multiple hydrogens in a residue just named 'H'). If this sounds like it could be your problem, download the daily build and use that. If you had used Help->Report A Bug to report the problem, I would have noticed this sooner. ;-) --Eric On Jun 22, 2015, at 12:44 PM, Eric Pettersen <pett@cgl.ucsf.EDU> wrote:
Hi Karl, We have not encountered this behavior. Do you have a session or PDB file where this happens reliably for you? If so, could you use Chimera's Help->Report A Bug and attach the file? I can keep the data private if that's an issue.
--Eric
Eric Pettersen UCSF Computer Graphics Lab http://www.cgl.ucsf.edu
On Jun 19, 2015, at 3:32 PM, Karl Sebby <karl.sebby@leftsideresearch.com> wrote:
Hi I am modifying several ligand/protein complexes; usually with the “Build Structures” tool. I modify ligands by changing and deleting atoms, or by using “Join Models” after building or importing a structure with “Start structure”. Sometimes, minimizing the ligand works fine, but other times I get the error: “Attribute Error: ‘AtomType’ object has no attribute ‘amber_atom_type’”. I cannot figure out what is causing this error or how to fix it. It seems to happen when I begin working from a saved session or a pdb that was written with the ‘write’ command and not when I go through a whole series of steps in one shot. Any ideas on what is going on? Thanks, All the best, Karl -- Dr Karl Sebby
Left Side Research LLC 1661 K M Ranch Road Whitefish Montana 59937 Office: 406 623 4773
_______________________________________________ Chimera-users mailing list Chimera-users@cgl.ucsf.edu http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users
_______________________________________________ Chimera-users mailing list Chimera-users@cgl.ucsf.edu http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users
participants (2)
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Karl Sebby