[chimera-dev] changing side chain atoms in Chimera

[Elaine Meng]

Dear Ouertani Awatef,

(2) A cysteine bridge is just a bond between the S atoms of two cysteine residues.  So if you already have the cysteine residues in a reasonable bonding position, just add a bond between those two atoms.  First display the atoms, for example these commands to display the atoms of all cysteine residues:

~ribbon
display :CYS

 If the residues have hydrogens, you have to delete the hydrogens from the -SH groups first, for example to delete all hydrogens is command:

delete H

Then you could select the two S atoms (for example, Ctrl-click one, Shift-Ctrl-click the second one) and add a bond, for example command:

bond sel

There is help for all of the above commands, for example use command "help bond" to see the help page for the bond command.

(2) Dehydration is not so simple.  You have to understand the chemical groups yourself and figure out which atoms to delete and which atoms to change atom type.  Deletion is described above for #1.  Changing type can be done with the Build Structure tool, Modify Structure section, see:
<https://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/editing/editing.html#build>

For future questions,  if you are just asking generally how to do something in Chimera, better to send to chimera-users at cgl.ucsf.edu ... this chimera-dev at cgl.ucsf.edu address is for programming questions (e.g. how to write python or other code for Chimera).

I hope this helps,
Elaine
-----
Elaine C. Meng, Ph.D.                       
UCSF Chimera(X) team
Department of Pharmaceutical Chemistry
University of California, San Francisco


> On Mar 16, 2023, at 6:27 AM, Ouertani Awatef via Chimera-dev <chimera-dev at cgl.ucsf.edu> wrote:
> 
> Dear all
> Good morning
> Please i would like to know :
> 1) how to make serine and threonine dehydration using chimera
> 2) how to make a cysteine-cysteine bridge using chimera 
> Many thanks