Mutated several residues (amino acids or nucleotides) at the same time
Hi there, I wondered if it would be possible to change several residues at the same time using the “swapna” and “swapaa” commands in order to change the model file so that it matches a target sequence. This would be extremely helpful for model building purposes. Many thanks, Matthias
Hi Matthias, You can already change multiple residues using a single "swap" command, but only if they will be the same final type. For example, something like: swapaa :phe,tyr his - or - swapaa /A:1-4 leu If you want to model a specific protein sequence that has a lot of differences from the original structure, but using that original structure as the template, the better approach would be with Modeller comparative modeling. That cannot be used for nucleic acids, however. <https://rbvi.ucsf.edu/chimerax/docs/user/tools/modeller.html> I.e. you would open the target sequence, make sure to associate it with the original structure if it is not already automatically associated, and then use the Modeller Comparative tool or "modeller comparative" command. <https://rbvi.ucsf.edu/chimerax/docs/user/commands/open.html#sequence> <https://rbvi.ucsf.edu/chimerax/docs/user/tools/sequenceviewer.html#associati...> <https://rbvi.ucsf.edu/chimerax/docs/user/tools/modeller.html> There are also AI prediction methods for peptide structure, e.g. "alphafold predict" "esmfold predict" albeit with better reliability on natural sequences rather than newly designed. <https://rbvi.ucsf.edu/chimerax/docs/user/tools/alphafold.html> <https://rbvi.ucsf.edu/chimerax/docs/user/tools/esmfold.html> If you need to stick with multiple "swap" commands (e.g. for nucleic or other reasons) it may be easier to create a command (.cxc) file in a text editor first and then simply open it to execute. <https://rbvi.ucsf.edu/chimerax/docs/user/commands/usageconventions.html#cxc-...> 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 8, 2023, at 1:50 AM, Vorländer,Matthias Kopano via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:
Hi there,
I wondered if it would be possible to change several residues at the same time using the “swapna” and “swapaa” commands in order to change the model file so that it matches a target sequence. This would be extremely helpful for model building purposes.
Many thanks, Matthias
Dear Elaine, Thanks a lot for your reply. I was unaware that modeler can be used directly from within chimeraX, that's great. Regarding the possibility to replace multiple residues to a different sequence using the swapna and swapaa commands, a text file is a workaround, but I think the implementation of a native feature would be a valuable addition for everyone who works with ChimeraX and Isolde for model building :) Many thanks, Matthias On 08.03.23, 17:29, "Elaine Meng" <meng@cgl.ucsf.edu> wrote: Hi Matthias, You can already change multiple residues using a single "swap" command, but only if they will be the same final type. For example, something like: swapaa :phe,tyr his - or - swapaa /A:1-4 leu If you want to model a specific protein sequence that has a lot of differences from the original structure, but using that original structure as the template, the better approach would be with Modeller comparative modeling. That cannot be used for nucleic acids, however. <https://rbvi.ucsf.edu/chimerax/docs/user/tools/modeller.html> I.e. you would open the target sequence, make sure to associate it with the original structure if it is not already automatically associated, and then use the Modeller Comparative tool or "modeller comparative" command. <https://rbvi.ucsf.edu/chimerax/docs/user/commands/open.html#sequence> <https://rbvi.ucsf.edu/chimerax/docs/user/tools/sequenceviewer.html#associati...> <https://rbvi.ucsf.edu/chimerax/docs/user/tools/modeller.html> There are also AI prediction methods for peptide structure, e.g. "alphafold predict" "esmfold predict" albeit with better reliability on natural sequences rather than newly designed. <https://rbvi.ucsf.edu/chimerax/docs/user/tools/alphafold.html> <https://rbvi.ucsf.edu/chimerax/docs/user/tools/esmfold.html> If you need to stick with multiple "swap" commands (e.g. for nucleic or other reasons) it may be easier to create a command (.cxc) file in a text editor first and then simply open it to execute. <https://rbvi.ucsf.edu/chimerax/docs/user/commands/usageconventions.html#cxc-...> 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 8, 2023, at 1:50 AM, Vorländer,Matthias Kopano via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote: > > Hi there, > > I wondered if it would be possible to change several residues at the same time using the “swapna” and “swapaa” commands in order to change the model file so that it matches a target sequence. This would be extremely helpful for model building purposes. > > Many thanks, > Matthias
Hi Matthias, Swapaa/na could be enhanced to allow multiple different swaps at once with a medium amount of effort. I will open an enhancement-request ticket in our bug tracking database for that, with you cc'ed. --Eric Eric Pettersen UCSF Computer Graphics Lab
On Mar 8, 2023, at 11:32 AM, Vorländer,Matthias Kopano via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:
Dear Elaine,
Thanks a lot for your reply. I was unaware that modeler can be used directly from within chimeraX, that's great.
Regarding the possibility to replace multiple residues to a different sequence using the swapna and swapaa commands, a text file is a workaround, but I think the implementation of a native feature would be a valuable addition for everyone who works with ChimeraX and Isolde for model building :)
Many thanks, Matthias
On 08.03.23, 17:29, "Elaine Meng" <meng@cgl.ucsf.edu> wrote:
Hi Matthias, You can already change multiple residues using a single "swap" command, but only if they will be the same final type. For example, something like:
swapaa :phe,tyr his - or - swapaa /A:1-4 leu
If you want to model a specific protein sequence that has a lot of differences from the original structure, but using that original structure as the template, the better approach would be with Modeller comparative modeling. That cannot be used for nucleic acids, however. <https://rbvi.ucsf.edu/chimerax/docs/user/tools/modeller.html>
I.e. you would open the target sequence, make sure to associate it with the original structure if it is not already automatically associated, and then use the Modeller Comparative tool or "modeller comparative" command.
<https://rbvi.ucsf.edu/chimerax/docs/user/commands/open.html#sequence> <https://rbvi.ucsf.edu/chimerax/docs/user/tools/sequenceviewer.html#associati...> <https://rbvi.ucsf.edu/chimerax/docs/user/tools/modeller.html>
There are also AI prediction methods for peptide structure, e.g. "alphafold predict" "esmfold predict" albeit with better reliability on natural sequences rather than newly designed. <https://rbvi.ucsf.edu/chimerax/docs/user/tools/alphafold.html> <https://rbvi.ucsf.edu/chimerax/docs/user/tools/esmfold.html>
If you need to stick with multiple "swap" commands (e.g. for nucleic or other reasons) it may be easier to create a command (.cxc) file in a text editor first and then simply open it to execute. <https://rbvi.ucsf.edu/chimerax/docs/user/commands/usageconventions.html#cxc-...>
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 8, 2023, at 1:50 AM, Vorländer,Matthias Kopano via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:
Hi there,
I wondered if it would be possible to change several residues at the same time using the “swapna” and “swapaa” commands in order to change the model file so that it matches a target sequence. This would be extremely helpful for model building purposes.
Many thanks, Matthias
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participants (3)
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Elaine Meng -
Eric Pettersen -
Vorländer,Matthias Kopano