makind disulfide bonds in Chimera x
Hello, Is it possible to make a disulfide bond between two Cys in spacial proximity and write it to the PDB file? Thank you Vladimir
Hello Vladimir, Yes, you can add a bond between two atoms. First show the atoms, then select the two that you want to bond (Ctrl-click on one, Shift-Ctrl-click on the second one so that both are highlighted in green), and then either (1) use the "bond" command, e.g. if the two atoms are selected you can specify them with "sel": bond sel If the atoms are deemed to be too far apart you may need to include "reasonable false" to make the bond anyway, see the help: <https://rbvi.ucsf.edu/chimerax/docs/user/commands/bond.html> - or - (2) use the Build Structure tool, the Adjust Bonds section (menu: Tools... Structure Editing... Build Structure) <https://rbvi.ucsf.edu/chimerax/docs/user/tools/buildstructure.html#bonds> I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Jun 2, 2023, at 11:58 AM, Vladimir Saudek via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:
Hello,
Is it possible to make a disulfide bond between two Cys in spacial proximity and write it to the PDB file?
Thank you
Vladimir
You can save the modified atomic structure as a PDB file with either the menu: File... Save, or the "save" command. <https://rbvi.ucsf.edu/chimerax/docs/user/commands/save.html#pdb> Elaine
On Jun 2, 2023, at 12:26 PM, Elaine Meng via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:
Hello Vladimir, Yes, you can add a bond between two atoms. First show the atoms, then select the two that you want to bond (Ctrl-click on one, Shift-Ctrl-click on the second one so that both are highlighted in green), and then either
(1) use the "bond" command, e.g. if the two atoms are selected you can specify them with "sel":
bond sel
If the atoms are deemed to be too far apart you may need to include "reasonable false" to make the bond anyway, see the help: <https://rbvi.ucsf.edu/chimerax/docs/user/commands/bond.html>
- or -
(2) use the Build Structure tool, the Adjust Bonds section (menu: Tools... Structure Editing... Build Structure)
<https://rbvi.ucsf.edu/chimerax/docs/user/tools/buildstructure.html#bonds>
I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Jun 2, 2023, at 11:58 AM, Vladimir Saudek via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:
Hello,
Is it possible to make a disulfide bond between two Cys in spacial proximity and write it to the PDB file?
Thank you
Vladimir
If you have ISOLDE installed, it also provides a tool to automatically form all “reasonable” (based on geometry) disulfides in a model. It’s not currently provided as a command, but it’s automatically run whenever you choose a model for ISOLDE to work on (it will bring up a dialogue box asking for confirmation if it finds anything). On Fri, 2 Jun 2023 at 20:27, Elaine Meng via ChimeraX-users < chimerax-users@cgl.ucsf.edu> wrote:
Hello Vladimir, Yes, you can add a bond between two atoms. First show the atoms, then select the two that you want to bond (Ctrl-click on one, Shift-Ctrl-click on the second one so that both are highlighted in green), and then either
(1) use the "bond" command, e.g. if the two atoms are selected you can specify them with "sel":
bond sel
If the atoms are deemed to be too far apart you may need to include "reasonable false" to make the bond anyway, see the help: <https://rbvi.ucsf.edu/chimerax/docs/user/commands/bond.html>
- or -
(2) use the Build Structure tool, the Adjust Bonds section (menu: Tools... Structure Editing... Build Structure)
<https://rbvi.ucsf.edu/chimerax/docs/user/tools/buildstructure.html#bonds>
I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Jun 2, 2023, at 11:58 AM, Vladimir Saudek via ChimeraX-users < chimerax-users@cgl.ucsf.edu> wrote:
Hello,
Is it possible to make a disulfide bond between two Cys in spacial proximity and write it to the PDB file?
Thank you
Vladimir
_______________________________________________ ChimeraX-users mailing list -- chimerax-users@cgl.ucsf.edu To unsubscribe send an email to chimerax-users-leave@cgl.ucsf.edu Manage subscription:
Many thanks. This is very useful for me. Best wishes. Vladimir On 02/06/2023 21:35, Tristan Croll wrote:
If you have ISOLDE installed, it also provides a tool to automatically form all “reasonable” (based on geometry) disulfides in a model. It’s not currently provided as a command, but it’s automatically run whenever you choose a model for ISOLDE to work on (it will bring up a dialogue box asking for confirmation if it finds anything).
On Fri, 2 Jun 2023 at 20:27, Elaine Meng via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:
Hello Vladimir, Yes, you can add a bond between two atoms. First show the atoms, then select the two that you want to bond (Ctrl-click on one, Shift-Ctrl-click on the second one so that both are highlighted in green), and then either
(1) use the "bond" command, e.g. if the two atoms are selected you can specify them with "sel":
bond sel
If the atoms are deemed to be too far apart you may need to include "reasonable false" to make the bond anyway, see the help: <https://rbvi.ucsf.edu/chimerax/docs/user/commands/bond.html>
- or -
(2) use the Build Structure tool, the Adjust Bonds section (menu: Tools... Structure Editing... Build Structure)
<https://rbvi.ucsf.edu/chimerax/docs/user/tools/buildstructure.html#bonds>
I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
> On Jun 2, 2023, at 11:58 AM, Vladimir Saudek via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote: > > Hello, > > Is it possible to make a disulfide bond between two Cys in spacial proximity and write it to the PDB file? > > Thank you > > Vladimir
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participants (3)
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Elaine Meng -
Tristan Croll -
Vladimir Saudek