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Topics - espinosaleal

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General discussions (Q&As) / About the mutation in DNA
« on: April 17, 2014, 05:24:13 pm »
I'm working on DNA homopolymers and I have a question about the 'mutate_bases' process. If I use 'fiber' to create a sequence, for example GGGG, the B-DNA structure will add automatically the complementary cytosines, in that case I obtain GC-GC-GC-GC. Because my interest is in DNA-homopolymers, I just use 'mutate_bases' to change the guanines for cytosines, to obtain CC-CC-CC-CC , but I always obtain a 'cisoid' configuration for the C-C pairs. I'd like to know if I can built a DNA-homopolymer sequence where the pairs have a 'transoid' configuration, is it possible?

Best regards,

leo

2
General discussions (Q&As) / one comment + one question
« on: February 22, 2013, 07:30:05 am »
Hi everybody

I've been using X3DNA (v2.1) the last days trying to learn how to build up some structures and I'm
really happy, there are a lot of things that i can do with this tool. Anyway, I have one comment and
one stupid question:
1. Comment: the option -single doesn´t work properly, you have to use -s instead.
2. Stupid question: how I can add the hydrogen atoms to my structure? Maybe there is
    a better way to do it than using for example Avogadro, because if you use this option
    the sistem also add the hydrogen atoms to the backbone.

Thanks a lot,

leonardo

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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.