3DNA Forum

Questions and answers => General discussions (Q&As) => Topic started by: Shreya Ghosh on April 18, 2020, 07:29:47 pm

Netiquette · Download · News · Gallery · G-quadruplexes · DSSR-Jmol · DSSR-PyMOL · Video Overview · DSSR v2.5.2 (DSSR Manual) · Homepage

Title: Generating PDB file
Post by: Shreya Ghosh on April 18, 2020, 07:29:47 pm

After creating a .par file, I tried to create a pdb.

I used the BuildNucleicAcids.py function and mentioned the DNA type and other details. It generated a pdb file without the DNA backbone atoms (attached image).

Could you please let me know how to generate a proper pdb file with the appropriate DNA backbone atoms?

Title: Re: Generating PDB file
Post by: xiangjun on April 18, 2020, 08:53:55 pm

Quote

I used the BuildNucleicAcids.py function and mentioned the DNA type and other details. It generated a pdb file without the DNA backbone atoms (attached image).

"BuildNucleicAcids.py" is not part of 3DNA. Please ask the author of the program for support.

Xiang-Jun

Funded by the NIH R24GM153869 grant on X3DNA-DSSR, an NIGMS National Resource for Structural Bioinformatics of Nucleic Acids

Created and maintained by Dr. Xiang-Jun Lu, Department of Biological Sciences, Columbia University