Question: Creating Bonds B/W 2 Pdb Structures
gravatar for Tofayel Ahmed
9.5 years ago by
Tofayel Ahmed40 wrote:

Can anybody suggest a tool/method for joining two domains of a protein (i.e., creating peptide bond between two PDB structures)? I know this could be done in UCSF Chimera (Build strc...under Tools...> Structure editing), but due to some unknown reason, its not working in my system.

Thanks in advanced.

pdb domain protein software • 3.3k views
ADD COMMENTlink modified 9.5 years ago by Neilfws49k • written 9.5 years ago by Tofayel Ahmed40

Could you please give some more details about your question. What file format are you using? Why are you taking this approach, etc?

ADD REPLYlink written 9.5 years ago by Burlappsack660

Thanks for responding. Sorry for the late reply. I have solved it myself. Actually, I modelled a membrane protein that has extracellular and transmembrane domains in it. But, in the model, those two domains were not aligned in proper orientation. So, I splited the EC and TM domain into two and saved as two PDB files. Then both the files were opened in CHIMERA; together and again saved as PDB. It gives a PDB file with both the domains in it. Then I opened the PDB file in notepad and deleted the lines b/w "ATOM" descriptns of model 1(EC)& model 2(TM). This gave me my desired domain orientation.

ADD REPLYlink written 9.5 years ago by Tofayel Ahmed40
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