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1

General discussions (Q&As) / Re: Rebuilding Z-DNA

« on: Today at 06:05:18 am »

Thank you for your quick responses!
My input structure is the PDB structure 1QBJ. It is a 6nt DNA. I have attached a picture. Without using the x3dna_utils, even without extending, the backbone cannot  be modelled due to the distance of O3' and P being over 4.5 and throws the following error. However, I also tested with the fiber model of Z-DNA to understand how it works with Z-DNA. I found that besides the backbone not being modelled which is because of the PDB dataset not being since I'm not using x3dna_utils, rebuild could model the bases as separate molecules. So, this is possibly the issue with my Z-DNA crystal structure model.

Another observation was, previously, for the crystal structure of BDNA complexed with the protein, I tried to manually extend the DNA in pymol but due to the terminal base positions, I could not properly build the double helix. But after analyze and rebuild, I could. So I assume it is due to standardization of the structure after rebuild. However, there is a problem with this method for Z-DNA. Even if I manage to standardize the structure, pymol does not offer building Z-DNA. So, I was wondering if I could add the extended DNA before rebuild. As you suggested, I modified the bp_step.par file since that is the file used as input for rebuild. Is that the correct way? I apologize if I am asking too many questions.   

2

General discussions (Q&As) / Re: Rebuilding Z-DNA

« on: Yesterday at 02:23:03 pm »

I have a PDB structure of Z-DNA-protein complex that I wanted to simulate. Before simulation, I wanted to make the DNA longer to avoid the issue of the protein interacting with any of the terminal bases. I can use the following commands to achieve this in case of B-DNA:

find_pair 1MNN.pdb 1mnn.bps
x3dna_utils cp_std bdna
rebuild -atomic bp_step.par extended_dna.pdb

But x3dna_utils does not take zdna as an argument so I was wondering how I can do it?

3

General discussions (Q&As) / Rebuilding Z-DNA

« on: Yesterday at 02:10:17 pm »

I was wondering if there is a way to rebuild Z-DNA with rebuild module in the local installation of x3DNA. I know it works for B-DNA and A-DNA and I can make a Z-DNA fiber model as well but I couldn't find a direct way to extend an existing Z-DNA structure. Is there a workaround which I can try? Thank you in advance.