Hello every one
I have two protein structures having different ligands but sequence are similar almost.
I aligned the two so that both ligands come together now I want to save the aligned structure as pdb file how I can do it with single sequence and both ligands?
The pdb file that I saved is having both sequences. please find it attached and suggest
Thank you
Just align both the proteins and then click on S (given downside of panel to show the residues) and just remove all the residues of any one protein but not the ligand and then go to file menu and export molecule in pdb format.
In your test.pdb file, the two proteins have different chain label. Therefore it is easy to delete one using the command:
remove chain B and polymer.protein
to remove the protein atoms of chain B, but leave the ligand in place.
Or you can write only one chain and both ligands to a new pdb file by specifying:
save newfile.pdb, ((test and polymer.protein) or (/test//A/NAP or /test//B/BG6 ))
You can delete the coordinated of the second protein chain manually by editing the pdb file in the text editor.
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