[chimera-dev] changing side chain atoms in Chimera

[Ouertani Awatef]

Many thanks for your response.
Cordially

On Thu, 16 Mar 2023 at 4:25 PM Elaine Meng <meng at cgl.ucsf.edu> wrote:

> 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
>
>
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