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Welcome > Feature requests
Mutate_Bases: Option to mutate all residues of the same type to another
xiangjun:
Hi Manish,
Thanks for your detailed responses to my follow-up questions. Presumably, such a back-and-forth conversational style should be the norm on an online forum. In practice, as one can see by browsing the 3DNA Forum, that is normally not the case. I sense users may just want a quick and straight answer to their questions, which are frequently not well defined. I then ask for clarifications, but oftentimes receive no responses.
--- Quote ---I am not sure if there are any available software tools for sugar mutations. However, please let me know if you find/are aware of any such tools for sugar mutations. It would be of great help to me.
--- End quote ---
I'm aware of the paper "Using internal and collective variables in Monte Carlo simulations of nucleic acid structures: Chain breakage/closure algorithm and associated Jacobians" by Heinz Sklenar et al. which may be relevant to the topic here.
--- Quote ---' Do you have a concrete example of such mutations? '- Yes, there are many examples of such mutations in literature. Please go through either of these links to have a rough idea of what I am trying to study:
1- https://onlinelibrary.wiley.com/doi/full/10.1002/cbic.201600385
2- https://pubs.acs.org/doi/10.1021/bi201710q
--- End quote ---
I will follow these two links and see what I can get. Since your request in on sugar mutations which is not covered by the 'mutate_bases' program in 3DNA v2.x, please start a new thread for future communications.
Best regards,
Xiang-Jun
xiangjun:
As a follow-up of the initial request "Mutate_Bases: Option to mutate all residues of the same type to another". In 3DNA v3, I've added a new program named x3dna-mutate which can do this and much more, by incorporating the DSSR annotations. Some examples:
--- Code: ---x3dna-mutate --mutation='to=A' -i=1ehz.pdb -o=1ehz-allA.pdb
x3dna-mutate --mutation='name=A to=G' -i=1ehz.pdb -o=1ehz-A2G.pdb
x3dna-mutate -m='to=A cond=hairpin' -i=1ehz.pdb -o=1ehz-hairpinsA.pdb
x3dna-mutate --m='name=A negate to=G' -i=1ehz.pdb -o=1ehz-nonA2G.pdb
x3dna-mutate --m='chain=A num=12 to=DT' -i=355d.pdb -o=355d_G12T.pdb
x3dna-mutate --m='num=12 to=DT; num=13 to=DA' -i=355d.pdb -o=355d_TA.pdb
--- End code ---
Xiang-Jun
xiangjun:
As a follow-up of this thread, DSSR 2.0 (to be released soon) contains a new module for in silico base mutations with great flexibility and convenance. It can mutate all of the A's to G's except for residue 5 and residue 7, for example.
The 'mutate_bases' program is obsoleted. No program named 'x3dna-mutate' will be distributed.
Xiang-Jun
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Created and maintained by Dr. Xiang-Jun Lu [律祥俊] (xiangjun@x3dna.org)
The Bussemaker Laboratory at the Department of Biological Sciences, Columbia University.
