you are assigning the Atom class attribute "name" to be "BC1". Therefore, whenever the "name" attribute is looked up in any Atom instance after that, it finds the class assignment first and uses that, which is why all the atoms seem to have the name BC1 afterward.

In Chimera, you can't create an Atom "directly" -- you have to have a Molecule instance, which in turn has a method for adding Atoms. One of the simpler ways of adding Atoms is to use chimera.molEdit.addAtom(). That function has a pretty good doc string describing its arguments. Before you can use that function though you need to create a Molecule and Residue instance to contain the Atom. Look at the _newModel and _newResidue methods of BuildStructure/__init__.py for example code for that.

There's a somewhat useful handout we made for a Chimera programming class this summer that you may want to look over. It's available as a link off the Chimera Programmer's Guide page: http://www.cgl.ucsf.edu/chimera/docs/ProgrammersGuide/index.html

Eric Pettersen

UCSF Computer Graphics Lab

http://www.cgl.ucsf.edu

On Oct 14, 2008, at 7:45 AM, Patrick Ladam wrote:

Hello to the list,
I start trying to write my first py code in chimera (not that easy
without too much doc strings) and have a first question to submit.

Here is what I am doing in IDLE:

import chimera
opened = chimera.openModels.open('1zik.pdb')

mol = opened[0]
for i in mol.atoms:
print i.name

N
CA
CB
CG
CD
.../...

# Now I want to instanciate an atom and set its name attribute:

at1=chimera.Atom
at1.name="BC1"
print at1.name
BC1

# Now I redo the previous loop:

for i in mol.atoms:
print i.name

BC1
BC1
BC1
BC1
BC1
BC1
BC1
BC1
BC1
BC1
BC1
BC1
.../...

They're all BC1!!!

How come ? My created atom 'at1' and my 'mol' are supposed to be
completely seperated objects no?

Can someone help, I am afraid I missed something really basic here...
Bye to all
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