[Chimera-users] when will NoResidueRotamersError be raised?

Elaine Meng meng at cgl.ucsf.edu
Thu Feb 13 08:46:59 PST 2014


My advice is to not worry about the python:  just look in the Model Panel to see the #N of the structure you want, and then use it in the command as explained in my first reply.

Elaine

On Feb 12, 2014, at 6:14 PM, Xiao-Bo Li <x22li at cs.uwaterloo.ca> wrote:

> When I open a model, using "chimera.openModels.open(pdbID, type='PDB'), I dont get one model, I actually get a list.  So I thought the #0 referred to this list.
> 
> So my question was about how to references one model in this list of models, vs different models opened using this python call for different PDB IDs.
> 
> XBL
> 
> On 14-02-12 07:56 PM, Elaine Meng wrote:
>> Wow, I don't know what my problem is today!  That link should have been to the Model Panel documentation:
>> 
>> <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/modelpanel.html>
>> 
>> The only other thing I can think of that you might have meant is that your proteins were two different chains in the same model.  In that case, you would include the chain ID in the specification, as in my earlier example.
>> 
>> Elaine
>> 
>> On Feb 12, 2014, at 4:51 PM, Elaine Meng wrote:
>> 
>>> Hi XBL,
>>> Maybe the confusing part is the word "model."  In Chimera, we just use that word to mean a structure with atomic coordinates, which could be from experiments (crystallography, NMR, etc. such as entries in the Protein Data Bank) or calculations (protein structure prediction, etc.). Essentially each structure file you open becomes one model:
>>> <http://hmg.oxfordjournals.org/content/23/4/949.long>
>>> 
>>> I was guessing that your two structures are "models" from the Chimera point of view.  If not, and I still didn't answer your question, feel free to write back.
>>> I hope this helps,
>>> Elaine
>>> 
>>> On Feb 12, 2014, at 3:50 PM, Elaine Meng wrote:
>>> 
>>>> On Feb 12, 2014, at 10:45 AM, Xiao-Bo Li wrote:
>>>> 
>>>>> Hi Elaine,
>>>>> If I have two different protein structure open (not models), how can I reference one of them using the commandline?  I want to mutate one of them not the other.
>>>>> Best,
>>>>> XBL
>>>> Hi XBL,
>>>> The command-line specifications of different models are #0, #1, etc. You can see in the Model Panel (in Favorites menu) which number goes with which structure.  Also, there may be different chains even in one structure.  For example, residue 15 in chain A of model 0 is specified with:
>>>> 
>>>> #0:15.A
>>>> 
>>>> Please see the atom-specification documentation for more details and several examples.
>>>> <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/frameatom_spec.html>
>>>> 
>>>> That page is also linked to "atom-spec" in the Usage line of the "swapaa" command description.
>>>> <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/swapaa.html>
>>>> 
>>>> You might also want to take a look at the "getting started - command line" tutorial.
>>>> <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/tutorials/getting_started.html>
>>>> 
>>>> Elaine
>>> 
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> 




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