Messages

1

General discussions (Q&As) / Re: mutate_bases problem

« on: June 27, 2012, 10:28:55 pm »

oh ok...thanks a lot..now i understood....

2

General discussions (Q&As) / Re: mutate_bases problem

« 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..

3

General discussions (Q&As) / Re: mutate_bases problem

« on: June 26, 2012, 10:53:27 am »

and i have the new version and am using the program directly...

4

General discussions (Q&As) / Re: mutate_bases problem

« 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...

5

General discussions (Q&As) / 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?