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
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Susan Tsutakawa