Creating bond between two selected atoms
Hi Chimera X, I hope you are well. I am a student at Swarthmore College and am currently trying to use Chimera X to covalently attach glycans to asparagine residues. I was able to get 3 out of 5 of the glycans attached by selecting both atoms > structure editing > build structure > adjust bonds > add reasonable bonds. I did the same process for the other 2 glycans and no bond was made. The log says bond sel, 0 bonds. The glycans are combined with the protein using the combine command. I believed it may be an issue with an unreasonable binding distance but when I moved the glycan closer, the bond still didn't work. What else should I try? Also, do you know why it is working for some glycans but not others? Best, Ellie Streeper
Hi Ellie, I'm told that the "reasonable" option checks for distance, i.e. within the expected bond length plus a bit of tolerance. However, be aware that even if you get a bond with that option turned on, the bond could still be unreasonable for various other reasons, such as poor angles, some atom has too many atoms total bonded to it, etc. <https://rbvi.ucsf.edu/chimerax/docs/user/tools/buildstructure.html#bonds> For your specific question, your choices are any of the following: (1) turn off the "reasonable" option (2) move the glycan before using "combine" so that the two atoms to be bonded are closer together (3) instead of doing the positioning yourself and then using "combine" to merge the models, use the "Join Models" section of Build Structure and specify bond length and angles as needed in the "Other Bond" settings. That will move the separate glycan model to generate the specified length and angle, merge it into the protein model, and form the bond. <https://rbvi.ucsf.edu/chimerax/docs/user/tools/buildstructure.html#join> I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Resource for Biocomputing, Visualization, and Informatics Department of Pharmaceutical Chemistry University of California, San Francisco
On Jun 14, 2024, at 12:28 PM, Eleanor Streeper via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:
Hi Chimera X,
I hope you are well. I am a student at Swarthmore College and am currently trying to use Chimera X to covalently attach glycans to asparagine residues. I was able to get 3 out of 5 of the glycans attached by selecting both atoms > structure editing > build structure > adjust bonds > add reasonable bonds. I did the same process for the other 2 glycans and no bond was made. The log says bond sel, 0 bonds. The glycans are combined with the protein using the combine command.
I believed it may be an issue with an unreasonable binding distance but when I moved the glycan closer, the bond still didn't work. What else should I try? Also, do you know why it is working for some glycans but not others?
Best, Ellie Streeper
Hi Elaine, Thank you for getting back to me! The information is very helpful. For the "join model" strategy you recommended, is there a way to do this to an atom with more than 1 bond? The software says the atom must be joined only to one other atom. Best, Ellie Streeper On Fri, Jun 14, 2024 at 4:26 PM Elaine Meng <meng@cgl.ucsf.edu> wrote:
Hi Ellie, I'm told that the "reasonable" option checks for distance, i.e. within the expected bond length plus a bit of tolerance. However, be aware that even if you get a bond with that option turned on, the bond could still be unreasonable for various other reasons, such as poor angles, some atom has too many atoms total bonded to it, etc.
<https://rbvi.ucsf.edu/chimerax/docs/user/tools/buildstructure.html#bonds>
For your specific question, your choices are any of the following:
(1) turn off the "reasonable" option
(2) move the glycan before using "combine" so that the two atoms to be bonded are closer together
(3) instead of doing the positioning yourself and then using "combine" to merge the models, use the "Join Models" section of Build Structure and specify bond length and angles as needed in the "Other Bond" settings. That will move the separate glycan model to generate the specified length and angle, merge it into the protein model, and form the bond. <https://rbvi.ucsf.edu/chimerax/docs/user/tools/buildstructure.html#join>
I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Resource for Biocomputing, Visualization, and Informatics Department of Pharmaceutical Chemistry University of California, San Francisco
On Jun 14, 2024, at 12:28 PM, Eleanor Streeper via ChimeraX-users < chimerax-users@cgl.ucsf.edu> wrote:
Hi Chimera X,
I hope you are well. I am a student at Swarthmore College and am currently trying to use Chimera X to covalently attach glycans to asparagine residues. I was able to get 3 out of 5 of the glycans attached by selecting both atoms > structure editing > build structure > adjust bonds > add reasonable bonds. I did the same process for the other 2 glycans and no bond was made. The log says bond sel, 0 bonds. The glycans are combined with the protein using the combine command.
I believed it may be an issue with an unreasonable binding distance but when I moved the glycan closer, the bond still didn't work. What else should I try? Also, do you know why it is working for some glycans but not others?
Best, Ellie Streeper
Hi Ellie, The two atoms that you select for Join Models will be *removed* (not bonded to each other). For example, if you wanted to form a C-C bond, you could add hydrogens first, then select an H on each C (indicating where you want the new bond to be) and those two selected H atoms would be obliterated and replaced with the new C-C bond. As it says in the help: <https://rbvi.ucsf.edu/chimerax/docs/user/tools/buildstructure.html#join> "The selection must include exactly one atom from each model; these two atoms will be deleted and replaced with the new bond. Each of the selected atoms must be bonded to only one other atom, and it is these two other atoms that will form the new bond." These OTHER non-deleted atoms mentioned in the sentence above (the C atoms in my example) could have more than one bond already. I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Resource for Biocomputing, Visualization, and Informatics Department of Pharmaceutical Chemistry University of California, San Francisco
On Jun 17, 2024, at 7:00 AM, Eleanor Streeper via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:
Hi Elaine,
Thank you for getting back to me! The information is very helpful. For the "join model" strategy you recommended, is there a way to do this to an atom with more than 1 bond? The software says the atom must be joined only to one other atom.
Best, Ellie Streeper
On Fri, Jun 14, 2024 at 4:26 PM Elaine Meng <meng@cgl.ucsf.edu> wrote: Hi Ellie, I'm told that the "reasonable" option checks for distance, i.e. within the expected bond length plus a bit of tolerance. However, be aware that even if you get a bond with that option turned on, the bond could still be unreasonable for various other reasons, such as poor angles, some atom has too many atoms total bonded to it, etc.
<https://rbvi.ucsf.edu/chimerax/docs/user/tools/buildstructure.html#bonds>
For your specific question, your choices are any of the following:
(1) turn off the "reasonable" option
(2) move the glycan before using "combine" so that the two atoms to be bonded are closer together
(3) instead of doing the positioning yourself and then using "combine" to merge the models, use the "Join Models" section of Build Structure and specify bond length and angles as needed in the "Other Bond" settings. That will move the separate glycan model to generate the specified length and angle, merge it into the protein model, and form the bond. <https://rbvi.ucsf.edu/chimerax/docs/user/tools/buildstructure.html#join>
I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Resource for Biocomputing, Visualization, and Informatics Department of Pharmaceutical Chemistry University of California, San Francisco
On Jun 14, 2024, at 12:28 PM, Eleanor Streeper via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:
Hi Chimera X,
I hope you are well. I am a student at Swarthmore College and am currently trying to use Chimera X to covalently attach glycans to asparagine residues. I was able to get 3 out of 5 of the glycans attached by selecting both atoms > structure editing > build structure > adjust bonds > add reasonable bonds. I did the same process for the other 2 glycans and no bond was made. The log says bond sel, 0 bonds. The glycans are combined with the protein using the combine command.
I believed it may be an issue with an unreasonable binding distance but when I moved the glycan closer, the bond still didn't work. What else should I try? Also, do you know why it is working for some glycans but not others?
Best, Ellie Streeper
Hi Elaine, Thank you so much for your help! This is very helpful. Best, Ellie On Mon, Jun 17, 2024 at 11:01 AM Elaine Meng <meng@cgl.ucsf.edu> wrote:
Hi Ellie, The two atoms that you select for Join Models will be *removed* (not bonded to each other). For example, if you wanted to form a C-C bond, you could add hydrogens first, then select an H on each C (indicating where you want the new bond to be) and those two selected H atoms would be obliterated and replaced with the new C-C bond.
As it says in the help: <https://rbvi.ucsf.edu/chimerax/docs/user/tools/buildstructure.html#join>
"The selection must include exactly one atom from each model; these two atoms will be deleted and replaced with the new bond. Each of the selected atoms must be bonded to only one other atom, and it is these two other atoms that will form the new bond."
These OTHER non-deleted atoms mentioned in the sentence above (the C atoms in my example) could have more than one bond already. I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Resource for Biocomputing, Visualization, and Informatics Department of Pharmaceutical Chemistry University of California, San Francisco
On Jun 17, 2024, at 7:00 AM, Eleanor Streeper via ChimeraX-users < chimerax-users@cgl.ucsf.edu> wrote:
Hi Elaine,
Thank you for getting back to me! The information is very helpful. For the "join model" strategy you recommended, is there a way to do this to an atom with more than 1 bond? The software says the atom must be joined only to one other atom.
Best, Ellie Streeper
On Fri, Jun 14, 2024 at 4:26 PM Elaine Meng <meng@cgl.ucsf.edu> wrote: Hi Ellie, I'm told that the "reasonable" option checks for distance, i.e. within the expected bond length plus a bit of tolerance. However, be aware that even if you get a bond with that option turned on, the bond could still be unreasonable for various other reasons, such as poor angles, some atom has too many atoms total bonded to it, etc.
< https://rbvi.ucsf.edu/chimerax/docs/user/tools/buildstructure.html#bonds>
For your specific question, your choices are any of the following:
(1) turn off the "reasonable" option
(2) move the glycan before using "combine" so that the two atoms to be bonded are closer together
(3) instead of doing the positioning yourself and then using "combine" to merge the models, use the "Join Models" section of Build Structure and specify bond length and angles as needed in the "Other Bond" settings. That will move the separate glycan model to generate the specified length and angle, merge it into the protein model, and form the bond. <https://rbvi.ucsf.edu/chimerax/docs/user/tools/buildstructure.html#join
I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Resource for Biocomputing, Visualization, and Informatics Department of Pharmaceutical Chemistry University of California, San Francisco
On Jun 14, 2024, at 12:28 PM, Eleanor Streeper via ChimeraX-users < chimerax-users@cgl.ucsf.edu> wrote:
Hi Chimera X,
I hope you are well. I am a student at Swarthmore College and am currently trying to use Chimera X to covalently attach glycans to asparagine residues. I was able to get 3 out of 5 of the glycans attached by selecting both atoms > structure editing > build structure > adjust bonds > add reasonable bonds. I did the same process for the other 2 glycans and no bond was made. The log says bond sel, 0 bonds. The glycans are combined with the protein using the combine command.
I believed it may be an issue with an unreasonable binding distance but when I moved the glycan closer, the bond still didn't work. What else should I try? Also, do you know why it is working for some glycans but not others?
Best, Ellie Streeper
participants (2)
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Elaine Meng -
Eleanor Streeper