I am running MD simulations for holoenzyme in Gromacs. The protein has four chains like A, B, C, D. After MD simulations, All the chains are showing as X chain in VMD and even in the PDB file.
It is difficult to visualize and analyses the interactions. Please share your thoughts to rename all the chain name X into A, B, C, D, respectively. It helps me a lot. Thanks
Hi
To alter the chain names of residues...
Open your .pdb file in PyMOL.
Click "Display" then click "Sequence".
Manually click and drag across the residues you wish to alter the chain name of.
In the PyMOL command line type:
alter (sel),chain='Z'
And press Enter/Return
Z is the chain name you want the selected residues to have and may be any letter.
Then in the command line type:
Rebuild
And press Enter/Return.
Repeat the process until you have divided the sequence up in your desired chain names.
Export your molecule as a .pdb file by clicking "File" then "Export Molecule" then "Save" and then choose .pdb file from the drop-down list of file types.
Hope it helps.
Tom
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