Creating Bonds B/W 2 Pdb Structures

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12.7 years ago

Tofayel Ahmed ▴ 40

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 protein domain software • 4.2k views

ADD COMMENT • link updated 12.7 years ago by Neilfws 49k • written 12.7 years ago by Tofayel Ahmed ▴ 40

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

ADD REPLY • link 12.7 years ago by Burlappsack ▴ 690

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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 REPLY • link 12.6 years ago by Tofayel Ahmed ▴ 40

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