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Author Topic: Mutate_Bases: Option to mutate all residues of the same type to another  (Read 2136 times)

Offline slaw

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Xiang-Jun,

I am playing with mutating 1RNA.pdb (contains only A/U) into a structure that contains only C/G (G for A and C for U).  This is not vital but it would be nice if there was an option to convert ALL of the A's to G's (or whatever is needed) and all of the U's to C's.  The current functionality is perfectly fine for a few point mutations but this added capability would be helpful and make the process less tedious having to create a file to list out all of the individual mutations.  I can also see a logical negation to be useful as well.  For example, mutate all of the A's to G's except for residue 5 and residue 7.

Again, the program works great so this would only be a wish-list request.

Thank you for your time, effort, and continued support of 3DNA!

Offline xiangjun

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Thanks for your request for adding new options to mutate_bases "to mutate all residues of the same type to another". I see your point, but I feel such functionality is better served by purpose-specific scripts instead of by mutate_bases itself. As a general design principle, I aim to make the core part of 3DNA focused, robust and efficient, and use Ruby scripts to build up features of general interest. Overall, 3DNA is intended as a toolset to be used as users see fit.

With regard to mutate_bases, I am considering to add an option to list all bases (nucleotides) in a PDB structure in a format that can be easily modified (either manually or pragmatically) and then fed back to the program. This option allows for easy adaptation of mutate_bases to various common situations (including yours), without adding too many bells and whistles that would blur the program's primary function.

An excerpt example for the first 12 bases of 6tna is as below:

Code: [Select]
chain=A snum=1 name=G
chain=A snum=2 name=C
chain=A snum=3 name=G
chain=A snum=4 name=G
chain=A snum=5 name=A
chain=A snum=6 name=U
chain=A snum=7 name=U
chain=A snum=8 name=U
chain=A snum=9 name=A
chain=A snum=10 name=2MG
chain=A snum=11 name=C
chain=A snum=12 name=U

Does this sound useful?

Xiang-Jun
« Last Edit: April 21, 2012, 10:12:18 am by xiangjun »
Dr. Xiang-Jun Lu [律祥俊]
Email: xiangjun@x3dna.org
Homepage: http://x3dna.org/
Forum: http://forum.x3dna.org/

 

Created and maintained by Dr. Xiang-Jun Lu[律祥俊]· Supported by the NIH grant R01GM096889 · Dr. Lu is currently a member of the Bussemaker Laboratory at the Department of Biological Sciences, Columbia University. The project is in collabration with the Olson Laborarory at Rutgers where 3DNA got started.