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Missing segments of protein and minimization

I have problem with pdb file when I want to use for docking becuase they have missing segments and it`s neccessary to minimize energy. I know for Chimera, SwissPDB and Modeller. I want to ask you which is better and how to work with it

software error
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updated by Ram Ram • written by chemistry1233 • chemistry1233

2 answers

You should use either MODELLER or another homology modelling / loop modelling software. Chimera and SwissPDB (Viewer) are visualisation tools and are not suited for this task. The energy minimisation can also be done with MODELLER (if you provide a complete protein and its sequence). Have a look at the manual and/or the tutorial.

To avoid installing and running it locally, you can use the MODELLER interface on the HHpred website.

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updated by Ram Ram • written by João Rodrigues João Rodrigues

Can anyone to tell step by step for add missing segments and minimization throught SwissPDB and Chimera

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written by chemistry1233 • chemistry1233

No. Besides the other answers, I pointed you to the HHpred website that does a pretty simple job at adding missing segments. You just need to learn the basics of homology modelling.

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updated by Ram Ram • written by João Rodrigues João Rodrigues

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