I have a pdb file. It is a mixture of alpha- tocopherol and a protein. I want to extract only the alpha-tocopherol. When I delete protein entries then there is a problem in the file. Please help me to extract it.
Hi,
unfortunately you do provide us with more information about your "problem in file".
In general it is easiest and also save to delete die respective entries via a text editor and save the new pdb; normally, programs only read the ATOM cards from a pdb file.
Under Linux/Unix you also could use the grep command to extract the tocopherol units.
Hope this helps.
Hi,
unfortunately you do provide us with more information about your "problem in file".
In general it is easiest and also save to delete die respective entries via a text editor and save the new pdb; normally, programs only read the ATOM cards from a pdb file.
Under Linux/Unix you also could use the grep command to extract the tocopherol units.
Hope this helps.
If you are using PyMol and you obtained the PDB file from the PDB:
- Go to the PDB website and find your file, scroll down to ligands, and make note of the three letter identifier for alpha-tocopherol. It should be something like 'VIV' or 'VIT'.
- Fetch the PDB file in pymol, then type 'sele not resn vit' (replace vit with identifier - this will select everything that is not identified as 'vit'.)
- Now type 'remove sele', that will remove the atoms in the current selection, leaving you only with the alpha-tocopherol.
- Go to 'file -> Save molecule', and save the molecule.
U can do the same thing what Maximilian said in discovery studio 3.5 client version. Its free....
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