[PyMOL] problems creating object using align method

[Sanaa Syed]

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!

[David Hall]

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

Post by Sanaa Syed
Hello,
list1=["chain_A","chain_B","chain_C","chain_D"]
cmd.load("/home/sanaa/pymol/"+every+".pdb")
object_list=cmd.get_object_list()
aligned=[ ]
list2=[ ]
#object=string(alignedA_B)
aligned=cmd.align(object_list[0],object_list[j+1],object=AlnAB)
list2.append(aligned)
pass
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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