Hi
I downloaded pdb file from rcsb and fixed missing residues by using Modeller. Now I have full dequence of pdb but few of the residue atoms are clashing with other backbone residues. How can I fix those overlaps. Kindly help.
I am unable to run docking without fixing these.
Kindly help!!
You can do a minimization with Chimera: Tools->Structure Edition->Minimize Structure. Pay attention that it is Chimera, not ChimeraX.
It's a crappy thing to do but what worked for me:
Manually resolving the clashes by editing the protein in PyMol and then doing
an energy minimization.
It is very likely that the energy minimization wont be able to resolve your clashes without doing that: If you pull it apart so that no atoms are positioned on top of each other and relax it in some energy function the minimizer will find a local minimum near to that position, which should be a configuration without clashes.
Thanks Ramin Ekhteiari Salmas and Benjamin E. Mayer
I resolved it by minimization
Hey Manoj Patel you can also fix the missing residues using CHARMM-GUI. Use the free plugin namely, PDB reader, I think that could also be helpful!
Best
Shubhashree
Thanks Shubhashree Barik for valuable advise. for as of now I resolved it by minimization as suggested by Ramin Ekhteiari Salmas .
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