Re: [PyMOL] problems creating object using align method

The error is due to you not surrounding AlnAB in quotes, so python treats it as a variable which has not been defined.

That said, align modifies the coordinates of the existing object, the object created just shows the correspondence of residues used for alignment. To save the superimposed coordinates, you use the existing objects.

-David

> On Mar 13, 2017, at 1:31 AM, Sanaa Syed <san...@gm...> wrote:
> 
> Hello,
> Can somebody please help me with creating aligned object using pymol API? i want   to split chains from my protein and superimpose first chain on the rest. the chains get loaded. and superimposed as well but i am unable to save superimposed coordinates in a new file because no object is created.  this is my script:
> list1=["chain_A","chain_B","chain_C","chain_D"]
> for every in list1:
>         cmd.load("/home/sanaa/pymol/"+every+".pdb")
> object_list=cmd.get_object_list()
> aligned=[ ]
> list2=[ ]
> #object=string(alignedA_B)
> for j in range(len(object_list)):
>        try:
>                         aligned=cmd.align(object_list[0],object_list[j+1],object=AlnAB)
>                         list2.append(aligned)
>         except IndexError:
>                 pass
> 
> this is giving me name error like:
> NameError: name 'AlnAB' is not defined
> 
> the object is not being created after calling the align command. it creates an object if i give the command directly on  pymol command line but not through the script. i have tried everything. please help!
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