I have successfully aligned the RNA structures in a colinear stacking way.
Thanks for the suggestions.
I am using "mergestr" command to write aligned structures in a PDB file.
Is it possible to renumber residues using the NAB command after mergestr?
I am trying to build protocol in the NAB script itself and thus, avoiding
external tools like pdb4amber for renumbering.
Thank you so much for the help!
On Thu, Jun 10, 2021 at 3:39 PM Mandar Kulkarni <
mandar.kulkarni.chem.gmail.com> wrote:
> Yes, I am trying to stack two duplexes.
>
> I planned to coincide the origin of the bottom duplex and top duplex so
> that they will stack over each other. then the top part will be translated
> and twisted via transformmol.
>
> But, I realized that these duplexes do not stack over each other with the
> above method.
>
> I guess I need to align the axes and then use transformmol to achieve
> this.
>
> Thanks and regards,
> Mandar Kulkarni
>
>
> On Thu, Jun 10, 2021 at 2:56 PM David A Case <david.case.rutgers.edu>
> wrote:
>
>> On Thu, Jun 10, 2021, Mandar Kulkarni wrote:
>> >
>> >Thanks for the suggestion about the alignframe and setframe.
>> >
>> >I tried this approach, without the common base "C" to connect two RNA
>> >duplexes. but the alignment issue is not solved. Please see attached NAB
>> >script and image.
>>
>> m = getpdb("rna_1.pdb");
>> setframe( 2, m, // aligning U4 from m1
>> ":4,U3:C6",
>> ":4,U3:C5", ":4,U3:N1",
>> ":4,U3:C6", ":4,U3:N3" );
>> alignframe( m, NULL );
>> putpdb( "std_m1.pdb", m );
>>
>> m = getpdb("rna_2.pdb");
>> setframe( 2, m, // aligning A1 from m2
>> ":1,A5:C4",
>> ":1,A5:C5", ":1,A5:N3",
>> ":1,A5:C4", ":1,A5:N1" );
>> alignframe( m, NULL );
>> putpdb( "std_m2.pdb", m );
>>
>>
>> The script above will put C6 of residue 4 of rna_1 at the origin, and it
>> will also put C4 of residue 1 of rna_2 at the origin (i.e. these two atoms
>> will be right on top of each other.) That is surely not what you want.
>>
>> It's hard to tell from what you've written what the desired outcome is.
>> Are you trying to make a co-linear stack of two duplexes? Once you get
>> the
>> helix axes along a desired direction, you would probably want to shift one
>> of the two helices along its helical axis, in order to displace them by a
>> certain amount.
>>
>> ...hope this helps....dac
>>
>>
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>>
>
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Received on Thu Jun 10 2021 - 14:00:02 PDT
