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1

General discussions (Q&As) / Re: Is there any tool to convert xyz file to pdb file that can be accepted by 3dna?

« on: April 10, 2019, 10:55:10 pm »

Hi Xiangjun,
I have noticed 3DNA can generate a starting DNA structure now. But, because I didn't know this when I was generating DNA structure, I chose another online tool to generate my structure, and used this structure to run a DFT calculation (with another software called ABACUS), which gave me the .cif file. Because of the DFT calculation, instead of generating a .pdb file from 3DNA, I have to find a method to convert this .cif file to a .pdb file. And because I thought .xyz file was easy to understand and edit, I chose to convert .cif file to .xyz file first, then convert .xyz file to .pdb file.
This is why I posted this topic, and I wish it may help others who have similar problems.

Best,
Erik

2

General discussions (Q&As) / Re: Is there any tool to convert xyz file to pdb file that can be accepted by 3dna?

« on: April 10, 2019, 04:12:54 pm »

Hello Xiangjun,
Sorry for replying late.
YES! You are right! It works! I haven't figured it out in a long time by myself, almost giving up.
I REALLY should have checked the forum earlier! You are a lifesaver, THANK YOU!
And to answer your question, my .xyz file was generated from a .cif file by VESTA. I have attached the .cif file below.

Best,
Erik

3

General discussions (Q&As) / Re: Is there any tool to convert xyz file to pdb file that can be accepted by 3dna?

« on: April 04, 2019, 01:34:55 am »

Hello Xiangjun,
Thanks for replying. I think my situation is not that bad. You will find that softwares like OpenBabel are more powerful than you think. OpenBabel can actually identify an atom's pdb name from an xyz file (Although I don't know how it is done. Pretty cool as I think). I have attached the pdb file that OpenBabel generated from my xyz file DNA_TypeA_12bp_1.xyz. It can mark the C atoms as C5*,  C4*, C8 etc, probably mean C5', C4', C8.
So I understand that I need to change symbols like C5* to C5', and do some other format changes. But do I need to add something like HEADER, TITLE,  COMPND, SOURCE etc to the converted pdb file? I want to use 3dna to calculate some geometry attributes like diameter, rise and twist of the DNA segment, so I think maybe these things like "HEADER" are not necessary. So can I leave these parts empty or do I have to fake them to make the pdb file acceptable by 3dna? Is there anything besides the "ATOM" part that will be actually used in 3dna in my case?
Best,
Erik

4

General discussions (Q&As) / Is there any tool to convert xyz file to pdb file that can be accepted by 3dna?

« on: April 03, 2019, 11:08:40 pm »

Hi Xiangjun,
I'm trying to convert an xyz file to a pdb file to use it in 3dna (I got the xyz file from other program which can not provide pdb file directly). I have tried VESTA and OpenBabel but they failed to create a pdb file that can be used in 3dna (although VESTA can work normally with these files). After a quick search I have found other similar problems posted before in the forum (like Topic: PDB conversion on: May 29, 2017, 06:49:35 am), but I have not found a quick solution to my problem. So I'm here to ask if there is any tool that can do the job.
My xyz file is attached below.
Best regards,
Erik