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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