Commands - bond angle and minimize
Hello all and Elaine, I am new here and would greatly appreciate Elaine and the Chimera Team, ChimeraX is so wonderful and you guys are not just providing the support to scientists, but advancing drug discovery and life science for humanity. Long story short, I have 3 problems in creating an enzyme-substrate model 1. I make a bond between the substrate and the enzyme, however, I could not make a right bond angle (kindly see the attached file, the bond angle between "Ser70 OG", "UNL1 C7", and "UNL1 O2", should be 120). I tried the command "bond angle", but don't know how to use it, and could not find the description about this command. How could this command be used? Could the bond angle be changed in Chimera? 2. 3. If the bond angle can be fixed, I need to eliminate any clashes before conducting energy minimization, however, the Tool "Rotamer" could not be applied to this covalently bound ligand. Is there some way to generate "rotamer" for this case? 4. 5. In the old version Chimera, there is a Tool called "minimize structure" and "Join Model (under "Build structure")" would it be any similar Tool in ChimeraX? 6. Again, thank you very much for your help. Cheers Kelvin Chung ABCT Department The Hong Kong Polytechnic University
Hello Kelvin, (1) the ChimeraX command to change angles is "angle" <https://rbvi.ucsf.edu/chimerax/docs/user/commands/angle.html> Example: angle :70@og:unl@c7,o2 120 move small However, then the other angles around C7 are ridiculous, and it won't necessarily work to keep going around and changing all 3 angles around C7 iteratively because for an sp2 carbon they should be 120 in the same plane as each other, but individual "angle" commands wouldn't necessarily enforce that. Instead, the workflow needed currently is to delete O2, redefine C7 as sp2 trigonal carbon, then add the O2 back. Namely: (A) select O2 (Ctrl-click on it), command: delete sel (B) Menu: Tools... Structure Editing... Build Structure, change from Start Structure to Modify Structure. Select C7 (Ctrl-click). Change settings to 3 bonds and trigonal geometry, leave residue name unchanged, click Apply. That will fill C7's valence with a hydrogen. Then select that hydrogen, change settings to O (oxygen), 1 bond, click Apply. <https://rbvi.ucsf.edu/chimerax/docs/user/tools/buildstructure.html#modify> Unfortunately (currently) if you just modify C7 settings without deleting the oxygen first, it won't do the bond angle rearrangement. (2) The Rotamers feature is only for standard amino acid sidechains. If you mean you want to change torsion angles, it can be done with the "torsion" command or by rotating bonds interactively by hand with the "bond rotation" mousemode, see <https://rbvi.ucsf.edu/chimerax/docs/user/commands/torsion.html> <https://rbvi.ucsf.edu/chimerax/docs/user/tools/mousemodes.html> E.g. to rotate a bond by hand, in the Right Mouse tab of the Toolbar across the top, click the icon for bond rotation, then use right mouse (= trackpad + Alt on Windows, trackpad + command on Mac) to click on the bond and drag vertically to change its rotation angle. <https://rbvi.ucsf.edu/chimerax/docs/user/tools/mousemodes.html> (3) sorry, ChimeraX does not yet have the equivalent of Chimera's Join Models or Minimize Structure. For those, you can still use Chimera, of course. I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Feb 25, 2022, at 1:00 AM, chung kelvin via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:
Hello all and Elaine,
I am new here and would greatly appreciate Elaine and the Chimera Team, ChimeraX is so wonderful and you guys are not just providing the support to scientists, but advancing drug discovery and life science for humanity.
Long story short, I have 3 problems in creating an enzyme-substrate model
• I make a bond between the substrate and the enzyme, however, I could not make a right bond angle (kindly see the attached file, the bond angle between "Ser70 OG", "UNL1 C7", and "UNL1 O2", should be 120). I tried the command "bond angle", but don't know how to use it, and could not find the description about this command. How could this command be used? Could the bond angle be changed in Chimera?
• If the bond angle can be fixed, I need to eliminate any clashes before conducting energy minimization, however, the Tool "Rotamer" could not be applied to this covalently bound ligand. Is there some way to generate "rotamer" for this case?
• In the old version Chimera, there is a Tool called "minimize structure" and "Join Model (under "Build structure")" would it be any similar Tool in ChimeraX?
Again, thank you very much for your help. Cheers
Kelvin Chung ABCT Department The Hong Kong Polytechnic University <enzyme with covalent substrate.cxs>
P.S. Thanks for your kind words! I got so busy answering the questions I forgot to say that :-) Best, Elaine
On Feb 25, 2022, at 8:48 AM, Elaine Meng via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:
Hello Kelvin, (1) the ChimeraX command to change angles is "angle" <https://rbvi.ucsf.edu/chimerax/docs/user/commands/angle.html>
Example: angle :70@og:unl@c7,o2 120 move small
However, then the other angles around C7 are ridiculous, and it won't necessarily work to keep going around and changing all 3 angles around C7 iteratively because for an sp2 carbon they should be 120 in the same plane as each other, but individual "angle" commands wouldn't necessarily enforce that.
Instead, the workflow needed currently is to delete O2, redefine C7 as sp2 trigonal carbon, then add the O2 back. Namely: (A) select O2 (Ctrl-click on it), command: delete sel (B) Menu: Tools... Structure Editing... Build Structure, change from Start Structure to Modify Structure. Select C7 (Ctrl-click). Change settings to 3 bonds and trigonal geometry, leave residue name unchanged, click Apply. That will fill C7's valence with a hydrogen. Then select that hydrogen, change settings to O (oxygen), 1 bond, click Apply. <https://rbvi.ucsf.edu/chimerax/docs/user/tools/buildstructure.html#modify>
Unfortunately (currently) if you just modify C7 settings without deleting the oxygen first, it won't do the bond angle rearrangement.
(2) The Rotamers feature is only for standard amino acid sidechains. If you mean you want to change torsion angles, it can be done with the "torsion" command or by rotating bonds interactively by hand with the "bond rotation" mousemode, see <https://rbvi.ucsf.edu/chimerax/docs/user/commands/torsion.html> <https://rbvi.ucsf.edu/chimerax/docs/user/tools/mousemodes.html>
E.g. to rotate a bond by hand, in the Right Mouse tab of the Toolbar across the top, click the icon for bond rotation, then use right mouse (= trackpad + Alt on Windows, trackpad + command on Mac) to click on the bond and drag vertically to change its rotation angle. <https://rbvi.ucsf.edu/chimerax/docs/user/tools/mousemodes.html>
(3) sorry, ChimeraX does not yet have the equivalent of Chimera's Join Models or Minimize Structure. For those, you can still use Chimera, of course.
I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Feb 25, 2022, at 1:00 AM, chung kelvin via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:
Hello all and Elaine,
I am new here and would greatly appreciate Elaine and the Chimera Team, ChimeraX is so wonderful and you guys are not just providing the support to scientists, but advancing drug discovery and life science for humanity.
Long story short, I have 3 problems in creating an enzyme-substrate model
• I make a bond between the substrate and the enzyme, however, I could not make a right bond angle (kindly see the attached file, the bond angle between "Ser70 OG", "UNL1 C7", and "UNL1 O2", should be 120). I tried the command "bond angle", but don't know how to use it, and could not find the description about this command. How could this command be used? Could the bond angle be changed in Chimera?
• If the bond angle can be fixed, I need to eliminate any clashes before conducting energy minimization, however, the Tool "Rotamer" could not be applied to this covalently bound ligand. Is there some way to generate "rotamer" for this case?
• In the old version Chimera, there is a Tool called "minimize structure" and "Join Model (under "Build structure")" would it be any similar Tool in ChimeraX?
Again, thank you very much for your help. Cheers
Kelvin Chung ABCT Department The Hong Kong Polytechnic University <enzyme with covalent substrate.cxs>
_______________________________________________ ChimeraX-users mailing list ChimeraX-users@cgl.ucsf.edu Manage subscription: https://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users
Dear Elaine, Sorry for the late reply, and greatly appreciate for your detail explanation and information. It is very helpful for my model building, the problem solved. Regards, Kelvin Chung ________________________________ 寄件者: Elaine Meng <meng@cgl.ucsf.edu> 寄件日期: 2022年2月26日 01:19 收件者: chung kelvin <wh-chung2@hotmail.com> 副本: ChimeraX Users Help <chimerax-users@cgl.ucsf.edu> 主旨: Re: [chimerax-users] Commands - bond angle and minimize P.S. Thanks for your kind words! I got so busy answering the questions I forgot to say that :-) Best, Elaine
On Feb 25, 2022, at 8:48 AM, Elaine Meng via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:
Hello Kelvin, (1) the ChimeraX command to change angles is "angle" <https://rbvi.ucsf.edu/chimerax/docs/user/commands/angle.html>
Example: angle :70@og:unl@c7,o2 120 move small
However, then the other angles around C7 are ridiculous, and it won't necessarily work to keep going around and changing all 3 angles around C7 iteratively because for an sp2 carbon they should be 120 in the same plane as each other, but individual "angle" commands wouldn't necessarily enforce that.
Instead, the workflow needed currently is to delete O2, redefine C7 as sp2 trigonal carbon, then add the O2 back. Namely: (A) select O2 (Ctrl-click on it), command: delete sel (B) Menu: Tools... Structure Editing... Build Structure, change from Start Structure to Modify Structure. Select C7 (Ctrl-click). Change settings to 3 bonds and trigonal geometry, leave residue name unchanged, click Apply. That will fill C7's valence with a hydrogen. Then select that hydrogen, change settings to O (oxygen), 1 bond, click Apply. <https://rbvi.ucsf.edu/chimerax/docs/user/tools/buildstructure.html#modify>
Unfortunately (currently) if you just modify C7 settings without deleting the oxygen first, it won't do the bond angle rearrangement.
(2) The Rotamers feature is only for standard amino acid sidechains. If you mean you want to change torsion angles, it can be done with the "torsion" command or by rotating bonds interactively by hand with the "bond rotation" mousemode, see <https://rbvi.ucsf.edu/chimerax/docs/user/commands/torsion.html> <https://rbvi.ucsf.edu/chimerax/docs/user/tools/mousemodes.html>
E.g. to rotate a bond by hand, in the Right Mouse tab of the Toolbar across the top, click the icon for bond rotation, then use right mouse (= trackpad + Alt on Windows, trackpad + command on Mac) to click on the bond and drag vertically to change its rotation angle. <https://rbvi.ucsf.edu/chimerax/docs/user/tools/mousemodes.html>
(3) sorry, ChimeraX does not yet have the equivalent of Chimera's Join Models or Minimize Structure. For those, you can still use Chimera, of course.
I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Feb 25, 2022, at 1:00 AM, chung kelvin via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:
Hello all and Elaine,
I am new here and would greatly appreciate Elaine and the Chimera Team, ChimeraX is so wonderful and you guys are not just providing the support to scientists, but advancing drug discovery and life science for humanity.
Long story short, I have 3 problems in creating an enzyme-substrate model
• I make a bond between the substrate and the enzyme, however, I could not make a right bond angle (kindly see the attached file, the bond angle between "Ser70 OG", "UNL1 C7", and "UNL1 O2", should be 120). I tried the command "bond angle", but don't know how to use it, and could not find the description about this command. How could this command be used? Could the bond angle be changed in Chimera?
• If the bond angle can be fixed, I need to eliminate any clashes before conducting energy minimization, however, the Tool "Rotamer" could not be applied to this covalently bound ligand. Is there some way to generate "rotamer" for this case?
• In the old version Chimera, there is a Tool called "minimize structure" and "Join Model (under "Build structure")" would it be any similar Tool in ChimeraX?
Again, thank you very much for your help. Cheers
Kelvin Chung ABCT Department The Hong Kong Polytechnic University <enzyme with covalent substrate.cxs>
_______________________________________________ ChimeraX-users mailing list ChimeraX-users@cgl.ucsf.edu Manage subscription: https://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users
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Elaine Meng