That would seem to violate rule #1 of macromolecular depiction:
Never change the coordinates!
But then I can't imagine why one would want to not draw a disulfide bond
in a real protein structure, so maybe this is some kind of exercise
where it is not important to adhere to the experimental results,
Hi Neshatul,
as Takanori already pointed out, PyMOL will bond those atoms based on distance
when loading the PDB file. So after unbonding and before writing the structure
out as a PDB file, you should change the coordinates of the cysteine sulfur
atoms. A neat way to accomplish this is to use P
Hi,
This is because PyMOL does not read SSBOND records
in PDB files. Actually, PyMOL determines if a bond
is present based on atomic distances and CONECT records.
http://www.pymolwiki.org/index.php/Connect_mode
PyMOL does not write SSBOND records when saving a
PDB file.
Best regards,
Takanori N
Hello every one,
I am not able save the pdb file, after I broke the disulfide bond.
what I did was
1-loaded the pdb file
2-selected 3-button editing mode
3-selected the two atoms bonded by disulfide bond
4-unbond pk1,pk2
Now it shows the bond break, but when I was saving the file without
disulfide
