I need to build a combination of two oligonucleotides which are complementary to each other through cytosine-cytosine base pairs. So I need to replace guanine with cytosine.
1. I load a PDB file.
2. I open Wizard and select Mutagenesis.
3. I select guanine residue in PyMol viewer.
4. Then I select "Mutate to cytosine" option.
5. I click on Apply and Done.
Then both guanine and cytosine residues disappear instead of replacement.
The mutation in the case of peptide is simple. There is even a tutorial video on youtube: https://www.youtube.com/watch?v=M-VCBz83nfs
In the case of nucleic acids the situation is different. Please, help!
Try X3DNA. By use of utility "fiber" you can build interactively the double helix in B-form of specified sequence. Just build 3'CCCC5' and 3'GGGG5', then remove complementary GGGG strands, like this:
fiber -b a.pdb (set CCCC)
fiber -b b.pdb (set GGGG)
Then remove from each file GGGG strands, and gather into one file remaining СССС strands.
I recommend using Maestro. It is very intuitive and it allows you to do a very short minimization of the replaced nucleotide as well.
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