I have one *.pdb file of protein. The * .pdb is composed of the complex of VEGF-A and VEGFR-2 D2,3. How can I separate it into forms VEGF-A and VEGFR-2 D2,3 in two pdb files? And what is the best way to find the two .pdbs with respect to each other?
If you use the PyMol program, you can save each chain separately:
- Go to the Displayand select Sequences to make Sequences appearing on the top of the PyMol viewer window.
- Go to the Display/Sequence Mode menu, and Select Chains, to make chains references appearing in place of the sequences.
- Click with the left button on one chain (A... B... etc) to select it and click with the right button to make a new menu apperaing.
- Select Action and Remove atoms to delete the chain.
- Save the remaining chain in a separate file and repaet it for the other chain to obtain your two subunit coordinate in separated files.
if you have downloaded the .txt file from PDB, you would see that each chain ends with a "TER" line which keeps continuity with the previous atom number. If you say, want to separate a *.pdb file containing chains A and B, into two *.pdb files containing only A and only B respectively, just delete the B chain coordinates and end with "TER" , "MASTER" and "END" lines for file a.pdb and vice-versa for b.pdb. You can open these two files in any viewer.
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