[Chimera-users] defining attribute

[Elaine Meng]

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/percentExposed.txt
> 
> 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>
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