Hi Alireza -
For renumbering a chain, the program PDBSET in the CCP4 suite is my tool of
choice. If your protein is chain A, the command would look something like this:
pdbset xyzin my_protein.pdb xyzout my_protein_renumbered.pdb EOF
renum 1 chain A
EOF
To remove the extraneous stuff within
Dear All,
I would like to colour different regions of a protein in different colour;
say region one, amino acid number 1 to 100 and region two amino acid 101 to
150; However, when I look into a pdb file using pymol; by displaying the
residuals, I see the residue number 1, does not correspond to
Hi,
There is a script available on the pymol wiki called zero_residues. This
will allow you to easily renumber any AA sequence.
As far as other heteroatoms are concerned you could consider removing them
(remove hetatm), or extract them into a second object.
Another alternative is to simply adjust
Thanks for your prompt answer,
numbers resets in every chain - and there is a lot of nucleobases in the
beginning (A,C,U,G) and MG at the end and these atoms mess up the residues
number additionally !
can I remove them via pymol ? Thank you
http://en.wikipedia.org/wiki/Nucleobase
On Sat, Dec 13,
