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Author Topic: mutate_bases problem  (Read 7771 times)

Offline khannakanika11

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mutate_bases problem
« on: June 26, 2012, 10:10:00 am »
Hi!

when i use the mutate_bases to lets change an A to C, then in pymol the sequences has DA but the mutated base is not DC it is just C. the problem i am getting is when i analyse it in your webserver, it shows these bases as non-watson pair. How to eliminate that?

Offline mauricio esguerra

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Re: mutate_bases problem
« Reply #1 on: June 26, 2012, 10:25:12 am »
Hi khannakanika11,

A little more background would help forum users to help with your problem.
For example, are you trying to mutate in an RNA structure or just plain double helical DNA?
Perhaps you have non-canonical Watson-Crick base-pairing in an RNA structure?

Also, it might be better to download 3dna new version 2.1 and use the mutate_bases program directly.

Cheers,

M.

Offline khannakanika11

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Re: mutate_bases problem
« Reply #2 on: June 26, 2012, 10:52:50 am »
Hi!

I am studying DNA-protein interactions...and these non-watson pairs dont result in the original output file on analysing the nucleic acid structure parameter summary file..thats why the confusion...

Offline khannakanika11

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Re: mutate_bases problem
« Reply #3 on: June 26, 2012, 10:53:27 am »
and i have the new version and am using the program directly...

Offline xiangjun

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Re: mutate_bases problem
« Reply #4 on: June 26, 2012, 01:31:04 pm »
Could you be more specific, showing a (minimum) reproducible example of the problem you are experiencing? Unless others know exactly what you are talking about, they won't be able to help solve your problem.

Xiang-Jun
Dr. Xiang-Jun Lu [律祥俊]
Email: xiangjun@x3dna.org
Homepage: http://x3dna.org/
Forum: http://forum.x3dna.org/

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Offline khannakanika11

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Re: mutate_bases problem
« Reply #5 on: June 27, 2012, 08:26:41 am »
Ok..I am working on the DNA-protein interactions on the protein 2R5Y.pdb
Using the web server of 3DNA when i generate the paramtere file of 2R5Y as it is i get the result attached.
But when i mutate the nucleotide no. 5 of chain C from T to G using mutate_bases of your version 2.1 , i generate a pdb 2R5Y-g5.pdb lets say and when i analyse this pdb using the web-server, i get the result of the parameter file attached. In this file, the mutated base G has a * and is shown to be a non-watson crick base pair. Now, why should this happen thats what i am asking? due to this i am not able to analyse my dna binding motif.

Please help..thanks..

Offline mauricio esguerra

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Re: mutate_bases problem
« Reply #6 on: June 27, 2012, 09:06:33 am »
Hi khannakanika11,

To see what's happening one can follow the next steps:

get_part -n 2r5y.pdb 2r5y_dna.pdb
mutate_bases 'c=c s=5 m=DG' 2r5y_dna.pdb 2r5y_mut.pdb

find_pair -p 2r5y_dna.pdb 2r5y_dna.inp
ex_str -4 bestpairs.pdb pair4original.pdb
stack2img -cdolt pair4original.pdb pair4original.ps

find_pair -p 2r5y_mut.pdb 2r5y_mut.inp
ex_str -4 allpairs.pdb pair4mutated.pdb
stack2img -cdolt pair4mutated.pdb pair4mutated.ps

You can see that the mutation creates a non-canonical G-A base-pair (see attached pic which is a merge of the two ps images created in the previous steps).

Perhaps your answer is just in using the -p option in find_pair, and then looking at the allpairs.ana file which can be given as input to analyze:

analyze allpairs.ana


Hope this helps,

Mauricio

Offline xiangjun

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Re: mutate_bases problem
« Reply #7 on: June 27, 2012, 06:12:21 pm »
In addition to Mauricio's suggestions, please note the following:

  • You do not need to run w3DNA -- the stand-alone version of 3DNA has all you need to perform your task. Specifically, mutate_bases is a new addition to 3DNA v2.1, not available from w3DNA yet.
  • The mutate_bases program can mutate a single base or any number of bases in a given structure. It just does what you ask it to do -- no more, no less. In particular, it does not check to maintain a Watson-Crick pair if you mutate only one the two bases.
  • The program can be run directly on a DNA-protein complex -- no need to first extract the DNA component.

If I understand you correctly, the following steps should explain and solve your puzzle:

Code: [Select]
# Download 2r5y from PDB. Let's call the file 2r5y.pdb
find_pair 2r5y.pdb stdout
    # you will see the Watson-Crick pair: C:...5_:[.DT]T-----A[.DA]:..37_:D
mutate_bases 'c=c s=5 m=DG' 2r5y.pdb 2r5y_c5_T2G.pdb
    # mutate only T5 on chain C (C.T5) to G, as specified. However, it does not mutate D.A37 to C
find_pair 2r5y_c5_T2G.pdb stdout
    # now you'd see: C:...5_:[.DG]G-**--A[.DA]:..37_:D  --- i.e., a G-A mispair
mutate_bases 'c=c s=5 m=DG; c=d s=37 m=DC' 2r5y.pdb 2r5y_c5_T2G_d37_A2C.pdb
    # here we explicitly mutate C.T5 --> G and D.A37 --> C
find_pair 2r5y_c5_T2G_d37_A2C.pdb stdout
    # now you have: C:...5_:[.DG]G-----C[.DC]:..37_:D

HTH,

Xiang-Jun
« Last Edit: June 27, 2012, 06:18:08 pm by xiangjun »
Dr. Xiang-Jun Lu [律祥俊]
Email: xiangjun@x3dna.org
Homepage: http://x3dna.org/
Forum: http://forum.x3dna.org/

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Offline khannakanika11

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Re: mutate_bases problem
« Reply #8 on: June 27, 2012, 10:28:55 pm »
oh ok...thanks a lot..now i understood....

 

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.