[Chimera-users] when will NoResidueRotamersError be raised?

Conrad Huang conrad at cgl.ucsf.edu
Thu Feb 13 09:24:14 PST 2014


You can use the "oslIdent" method for a model.  For example, to print 
the ids of the models opened and color the first one red, you can do:

import chimera
modelList = chimera.openModels.open(pdbID, type="PDB")
for m in modelList:
	print m.oslIdent()
cmd = "color red %s" % modelList[0].oslIdent()
chimera.runCommand(cmd)

Conrad

On 2/12/2014 6:14 PM, Xiao-Bo Li 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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