I am currently facing two transformational issues. Suppose I am given a protein's residue sequence and calpha distance matrix; is there a way to generate the 3d coordinates of the protein's residues from this information(I think there theoretically should be since it is a bijection up to rotation/translation). The second issue I am faced with is generating pdb files. How does one make a pdb file given the coordinates of the protein's residues along with the sequence? Is this enough information?

  • $\begingroup$ We have two questions here: the first one is geometrical rather than biological, the second one would be perhaps better to ask on bioinformatics.SE, but shortly, if you have only coordinates of Cα atoms you can only write a PDB file with coordinates of Cα atoms only. $\endgroup$ – marcin May 12 '19 at 7:58
  • $\begingroup$ Concerning the second issue, an easy way is described here. By the way, it is a quite common manipulation under Python, but finding a library can present few difficulties. Concerning the first issue, some advanced features library (such as PyRosetta) shall help you. $\endgroup$ – Elie Ker Arno Jun 26 '19 at 14:01
  • $\begingroup$ @ElieKerArno - Welcome. A link-only answer is not considered an answer. An answer should be self-containing and self-explanatory. Mentioning a source however is great practice. I'm converting this to a comment, but feel free to expand on your comment and post a new improved answer. Check out the help center on answering questions. $\endgroup$ – AliceD Jun 26 '19 at 20:49

Your Answer

By clicking “Post Your Answer”, you agree to our terms of service, privacy policy and cookie policy

Browse other questions tagged or ask your own question.