On Dec 18, 2007, at 10:40 AM, Jean-Didier Maréchal wrote:

Hi again,

I'd like to return the sequence of the protein I opened in chimera in the python shell.

...

From what I read through, I thought that chimera.getSequence could be used to do so.

I was thinking in a simple script beginning with : import chimera s=chimera.getSequence(0,0) ..

However the chimera.getSequence(0,0) comes back with:

Traceback (most recent call last): File "<pyshell#50>", line 1, in ? chimera.getSequence(0, 0) File "CHIMERA/share/chimera/Sequence.py", line 614, in getSequence File "CHIMERA/share/chimera/Sequence.py", line 656, in getSequences AttributeError: 'int' object has no attribute 'residues'

and

chimera.getSequence(0,A)

with

Traceback (most recent call last): File "<pyshell#48>", line 1, in ? chimera.getSequence(0,A) NameError: name 'A' is not defined

Did I understand correctly the role of getSequence? if yes, what would be the correct syntax please?

Hi JD, getSequence takes two arguments: a Molecule instance and a string containing a chain ID. It looks like you were trying to provide a model number and a chain ID of A. The chain needed to be a string and not just the bare letter A, which is interpreted as a variable named A by the Python interpreter (and which you undoubtedly haven't previously defined). You get a Molecule instance by using chimera.openModels.list to list Models and grab the one you want from that list. Something like: from chimera import openModels, Molecule m = openModels.list(id=0, modelTypes=[Molecule])[0] to get the Molecule open as model 0. Once you have the Molecule instance you don't even have to use getSequence, just: m.sequence("A") will return the Sequence object. --Eric Eric Pettersen UCSF Computer Graphics Lab http://www.cgl.ucsf.edu