[PyMOL] Finding RNA/DNA complementary base pairs using PyMOL

[Paweł Tomaszewski]

Dear all,
Is there a function or script which in simple way can find a complementary
base-pairs in my (deoxy)ribonucleic acid?

Suppose I have some double stranded RNA/DNA structure loaded into PyMOL.
Now I've chosen some nocleotyde or set of many nucleotydes and just want to
find residues of its complementary base-pairs (A-T, A-U, C-G).

Thanks a lot,
Paweł
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Re: [PyMOL] problems creating object using align method

[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

> On Mar 13, 2017, at 1:31 AM, Sanaa Syed  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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[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!
--
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