Specific residues to fix

We fix residues involved in activity/binding to reduce the probability to harm protein function during the process.
Fixed residues are not allowed to mutate or change conformation.

Here you have the opportunity to add pdb numbers of residues involved in activity/binding and could not be included through the "Small-molecule ligands" or in "Interacting chains" options.

These residues may include:

  1. Residues that are known to be important according to the literature.
  2. Residues that add information about binding/catalysis from other structures.

(the relevant numbers are the ones in the submitted pdb file)
If you enter a number that does not exist in the pdb, the query will crash. If the number exists but refers to the wrong residue, you are fixing an unnecessary residue reducing your options while not fixing the one you really meant to fix.

I know that residue X is important for function. Is there an easy way to include residues surrounding residue X?
Yes. You need to use PyMOL for this. See here a link to a short movie explaining how
https://www.youtube.com/watch?v=MknZuFm9ptE Note that there is a free version of PyMOL for students.

How do I extract relevant residues from another structure and find the matching ones in the structure I submit?
We prepared a movie to demonstrates this point through a common scenario. To watch the movie click here.

In all movies we used the 3 following commands: