Friends, I want to define solvent accessibility as the attribute to create a worm representation. I used the template file 'percentExposed.txt' in the following link to create an attribute file. The sample file i creased is attached (exp.txt) http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/defineattrib/percen... when i give the command: deffattr exp.txt I get the following error. How to resolve the problem. Traceback (most recent call last): File "/usr/local/chimera_15/lib/python2.6/site-packages/Pmw/Pmw_1_3/lib/PmwBase.py", line 1747, in __call__ return apply(self.func, args) File "/usr/local/chimera_15/share/Midas/midas_ui.py", line 260, in processCommand midas_text.makeCommand(text) File "/usr/local/chimera_15/share/Midas/midas_text.py", line 66, in makeCommand f(c, args) File "/usr/local/chimera_15/share/AddAttr/ChimeraExtension.py", line 33, in cmdAddAttr specInfo=[("spec", "models", "molecules")]) File "/usr/local/chimera_15/share/Midas/midas_text.py", line 424, in doExtensionFunc extFunc(*tuple(processedArgs), **kw) File "/usr/local/chimera_15/share/AddAttr/__init__.py", line 77, in addAttributes return _addAttr(attrFile, models, log, raiseTool) File "/usr/local/chimera_15/share/AddAttr/__init__.py", line 239, in _addAttr from ShowAttr import ShowAttrDialog, screenedAttrs ImportError: cannot import name screenedAttrs ImportError: cannot import name screenedAttrs File "/usr/local/chimera_15/share/AddAttr/__init__.py", line 239, in _addAttr from ShowAttr import ShowAttrDialog, screenedAttrs
Hi Bala, In both production release version 1.4.1 and a recent daily build (Sept 10), when I try to use the exp.txt file you sent, I did not get a traceback, but the error message: Data line 5 of file either not selector/value or not tab-delimited The original file in the documentation worked OK. I text-edited exp.txt to see the problem. In the line for residue 5, there are spaces in addition to the tabs. The data line should just be: (tab)atomspec(tab)value but on that line there was another space between the atomspec and the value, and also spaces after the value. After I removed those spaces, it worked fine, see attached file exp2.txt (it may be necessary to use Refresh....Menus in the Render tool if you had some failed attempts before that). I put the file on my mac Desktop, so for me the commands to open a sample structure and assign the attribute were open 121p defattr ~/Desktop/exp2.txt I hope this helps, 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 Sep 17, 2010, at 8:19 AM, Bala subramanian wrote:
Friends,
I want to define solvent accessibility as the attribute to create a worm representation. I used the template file 'percentExposed.txt' in the following link to create an attribute file. The sample file i creased is attached (exp.txt)
http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/defineattrib/percen...
when i give the command: deffattr exp.txt I get the following error. How to resolve the problem.
Traceback (most recent call last): File "/usr/local/chimera_15/lib/python2.6/site-packages/Pmw/Pmw_1_3/lib/PmwBase.py", line 1747, in __call__ return apply(self.func, args) File "/usr/local/chimera_15/share/Midas/midas_ui.py", line 260, in processCommand midas_text.makeCommand(text) File "/usr/local/chimera_15/share/Midas/midas_text.py", line 66, in makeCommand f(c, args) File "/usr/local/chimera_15/share/AddAttr/ChimeraExtension.py", line 33, in cmdAddAttr specInfo=[("spec", "models", "molecules")]) File "/usr/local/chimera_15/share/Midas/midas_text.py", line 424, in doExtensionFunc extFunc(*tuple(processedArgs), **kw) File "/usr/local/chimera_15/share/AddAttr/__init__.py", line 77, in addAttributes return _addAttr(attrFile, models, log, raiseTool) File "/usr/local/chimera_15/share/AddAttr/__init__.py", line 239, in _addAttr from ShowAttr import ShowAttrDialog, screenedAttrs ImportError: cannot import name screenedAttrs ImportError: cannot import name screenedAttrs
File "/usr/local/chimera_15/share/AddAttr/__init__.py", line 239, in _addAttr from ShowAttr import ShowAttrDialog, screenedAttrs
<exp.txt>
Hi Bala, This problem was fixed about 5 weeks ago, so if you get a current daily build it will work (though you will also have to make the changes that Elaine suggests in her email). --Eric Eric Pettersen UCSF Computer Graphics Lab http://www.cgl.ucsf.edu On Sep 17, 2010, at 8:19 AM, Bala subramanian wrote:
Friends,
I want to define solvent accessibility as the attribute to create a worm representation. I used the template file 'percentExposed.txt' in the following link to create an attribute file. The sample file i creased is attached (exp.txt)
http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/defineattrib/percen...
when i give the command: deffattr exp.txt I get the following error. How to resolve the problem.
Traceback (most recent call last): File "/usr/local/chimera_15/lib/python2.6/site-packages/Pmw/ Pmw_1_3/lib/PmwBase.py", line 1747, in __call__ return apply(self.func, args) File "/usr/local/chimera_15/share/Midas/midas_ui.py", line 260, in processCommand midas_text.makeCommand(text) File "/usr/local/chimera_15/share/Midas/midas_text.py", line 66, in makeCommand f(c, args) File "/usr/local/chimera_15/share/AddAttr/ChimeraExtension.py", line 33, in cmdAddAttr specInfo=[("spec", "models", "molecules")]) File "/usr/local/chimera_15/share/Midas/midas_text.py", line 424, in doExtensionFunc extFunc(*tuple(processedArgs), **kw) File "/usr/local/chimera_15/share/AddAttr/__init__.py", line 77, in addAttributes return _addAttr(attrFile, models, log, raiseTool) File "/usr/local/chimera_15/share/AddAttr/__init__.py", line 239, in _addAttr from ShowAttr import ShowAttrDialog, screenedAttrs ImportError: cannot import name screenedAttrs ImportError: cannot import name screenedAttrs
File "/usr/local/chimera_15/share/AddAttr/__init__.py", line 239, in _addAttr from ShowAttr import ShowAttrDialog, screenedAttrs
<exp.txt>_______________________________________________ Chimera-users mailing list Chimera-users@cgl.ucsf.edu http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users
Thank you Elaine and Eric, I am downloading the latest version. I have two rna duplexes. For each of them, i have calculated sasa values and i want to use this as my attribute ie sasa1.txt for duplex 1 and sasa2.txt for duplex2. Can i tell this catogorically to chimera. Im scared that chimera should nt interchange or apply same .txt to both molecules. Bala On Fri, Sep 17, 2010 at 7:01 PM, Eric Pettersen <pett@cgl.ucsf.edu> wrote:
Hi Bala, This problem was fixed about 5 weeks ago, so if you get a current daily build it will work (though you will also have to make the changes that Elaine suggests in her email).
--Eric
Eric Pettersen UCSF Computer Graphics Lab http://www.cgl.ucsf.edu
On Sep 17, 2010, at 8:19 AM, Bala subramanian wrote:
Friends,
I want to define solvent accessibility as the attribute to create a worm representation. I used the template file 'percentExposed.txt' in the following link to create an attribute file. The sample file i creased is attached (exp.txt)
http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/defineattrib/percen...
when i give the command: deffattr exp.txt I get the following error. How to resolve the problem.
Traceback (most recent call last): File "/usr/local/chimera_15/lib/python2.6/site-packages/Pmw/Pmw_1_3/lib/PmwBase.py", line 1747, in __call__ return apply(self.func, args) File "/usr/local/chimera_15/share/Midas/midas_ui.py", line 260, in processCommand midas_text.makeCommand(text) File "/usr/local/chimera_15/share/Midas/midas_text.py", line 66, in makeCommand f(c, args) File "/usr/local/chimera_15/share/AddAttr/ChimeraExtension.py", line 33, in cmdAddAttr specInfo=[("spec", "models", "molecules")]) File "/usr/local/chimera_15/share/Midas/midas_text.py", line 424, in doExtensionFunc extFunc(*tuple(processedArgs), **kw) File "/usr/local/chimera_15/share/AddAttr/__init__.py", line 77, in addAttributes return _addAttr(attrFile, models, log, raiseTool) File "/usr/local/chimera_15/share/AddAttr/__init__.py", line 239, in _addAttr from ShowAttr import ShowAttrDialog, screenedAttrs ImportError: cannot import name screenedAttrs ImportError: cannot import name screenedAttrs
File "/usr/local/chimera_15/share/AddAttr/__init__.py", line 239, in _addAttr from ShowAttr import ShowAttrDialog, screenedAttrs
<exp.txt>_______________________________________________ Chimera-users mailing list Chimera-users@cgl.ucsf.edu http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users
Hi Bala, You can include a model number in the first column of the data lines in the attribute file -- then just make sure you open the structures so that the right one goes with the right attribute file, i.e. that it has that model number. 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 Sep 17, 2010, at 10:54 AM, Bala subramanian wrote:
Thank you Elaine and Eric,
I am downloading the latest version. I have two rna duplexes. For each of them, i have calculated sasa values and i want to use this as my attribute ie sasa1.txt for duplex 1 and sasa2.txt for duplex2. Can i tell this catogorically to chimera. Im scared that chimera should nt interchange or apply same .txt to both molecules.
Bala
participants (3)
-
Bala subramanian -
Elaine Meng -
Eric Pettersen