I am opening up a pdb that has been generated after MD simulations. Waters have been removed. I am getting an unusual error. I have two pdb files that were generated similarly, but only one gives me the error. Traceback (most recent call last): File "/Applications/Chimera.app/Contents/Resources/share/chimera/tkgui.py", line 343, in openPath mols = chimera.openModels.open(path, type=ftype) File "/Applications/Chimera.app/Contents/Resources/share/chimera/__init__.py", line 1541, in open models = func(filename, *args, **kw) File "/Applications/Chimera.app/Contents/Resources/share/chimera/__init__.py", line 770, in _openPDBModel errOut=errLog) error: radius must be positive Error reading bfactor-911_changed.pdb: error: radius must be positive File "/Applications/Chimera.app/Contents/Resources/share/chimera/__init__.py", line 770, in _openPDBModel errOut=errLog) If someone can help, I would appreciate it.
HI Susan, The better approach to reporting Chimera problems is to use "Help... Report a Bug" in the Chimera menu and attach your input file (and include your email address if you would like feedback). Just showing the error message is usually not enough information. Thanks, Elaine ---------- Elaine C. Meng, Ph.D. UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco On Nov 28, 2011, at 12:52 PM, Susan Tsutakawa wrote:
I am opening up a pdb that has been generated after MD simulations. Waters have been removed.
I am getting an unusual error. I have two pdb files that were generated similarly, but only one gives me the error.
Traceback (most recent call last): File "/Applications/Chimera.app/Contents/Resources/share/chimera/tkgui.py", line 343, in openPath mols = chimera.openModels.open(path, type=ftype) File "/Applications/Chimera.app/Contents/Resources/share/chimera/__init__.py", line 1541, in open models = func(filename, *args, **kw) File "/Applications/Chimera.app/Contents/Resources/share/chimera/__init__.py", line 770, in _openPDBModel errOut=errLog) error: radius must be positive Error reading bfactor-911_changed.pdb: error: radius must be positive
File "/Applications/Chimera.app/Contents/Resources/share/chimera/__init__.py", line 770, in _openPDBModel errOut=errLog)
If someone can help, I would appreciate it.
Thanks. Will do that. Susan On Nov 28, 2011, at 2:02 PM, Elaine Meng wrote:
HI Susan, The better approach to reporting Chimera problems is to use "Help... Report a Bug" in the Chimera menu and attach your input file (and include your email address if you would like feedback). Just showing the error message is usually not enough information. Thanks, Elaine ---------- Elaine C. Meng, Ph.D. UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco
On Nov 28, 2011, at 12:52 PM, Susan Tsutakawa wrote:
I am opening up a pdb that has been generated after MD simulations. Waters have been removed.
I am getting an unusual error. I have two pdb files that were generated similarly, but only one gives me the error.
Traceback (most recent call last): File "/Applications/Chimera.app/Contents/Resources/share/chimera/tkgui.py", line 343, in openPath mols = chimera.openModels.open(path, type=ftype) File "/Applications/Chimera.app/Contents/Resources/share/chimera/__init__.py", line 1541, in open models = func(filename, *args, **kw) File "/Applications/Chimera.app/Contents/Resources/share/chimera/__init__.py", line 770, in _openPDBModel errOut=errLog) error: radius must be positive Error reading bfactor-911_changed.pdb: error: radius must be positive
File "/Applications/Chimera.app/Contents/Resources/share/chimera/__init__.py", line 770, in _openPDBModel errOut=errLog)
If someone can help, I would appreciate it.
participants (2)
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Elaine Meng -
Susan Tsutakawa