Re: [Chimera-users] Help and guidance on using chimera
Hi Tommy,
Sure those things can be easily be done. I'd encourage you to use ChimeraX instead of the old Chimera program. Also best to email questions to the Chimera mailing list (chimera-users@cgl.ucsf.edu mailto:chimera-users@cgl.ucsf.edu) or ChimeraX mailing list (chimerax-users@cgl.ucsf.edu mailto:chimerax-users@cgl.ucsf.edu).
To delete a domain of a protein in ChimeraX that is say residues 151 to 375 of chain B
delete /B:151-375
The command syntax would be different in Chimera. To add short linkers is more difficult and I will leave that question to Elaine to advise on the mailing list -- I am not the most knowledgable about how to do that.
Tom
On Apr 26, 2022, at 4:45 PM, Tommy Tong ttong@SDBRI.ORG wrote:
Dear Thomas, Good afternoon. How are you? My name is Tommy from San Diego Biomedical Research Institute, CA. I am new to Chimera software and my level of usage has been at the basic level, eg selecting chains and to color label the specific region on the protein.
May I ask if there is a way to selectively deleting a specific domain on a protein from a pdb file? I want to show graphically how the structure of the molecule will look like without the domain(s). In addition, is it possible to add short amino acid sequence, such as short linkers (eg GSGS) after a domain has been deleted from the protein structure?
I am currently using UCSF Chimera version 1.16.
Your help and advice are greatly appreciated. Thank you for your time.
Sincerely, Tommy
Hi Tommy, Currently I would still use Chimera (rather than ChimeraX) for building a short linker because it has a command to add amino acids one at a time to the end of a chain.
Chimera command "addaa": https://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/addaa.html
Example to add tyrosine as residue number 30 after residue 29 at the end of chain A: addaa tyr,30 :29.A
You can also delete residues in Chimera. The analogous Chimera command to Tom's ChimeraX example is: delete :151-375.B
If you simply want to hide part of a structure, you can just hide it rather than deleting it, e.g. Chimera commands ~disp :151-375.B ~ribbon :151-375.B
However, I understand that if you wanted to append a linker you really need to delete that other part first.
This page explains how to specify models, chains, residues, atoms in the Chimera command line: https://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/frameatom_spec.html
Then if you want to join the model that has the linker with another protein opened as a separate model, see Chimera's Build Structure tool (menu: Tools... Structure Editing... Build Structure), the Join Models section. See the help: https://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/editing/editing.html https://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/editing/editing.html#join
We are just now adding join models to ChimeraX, but it does not yet have anything like addaa.
I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Apr 26, 2022, at 6:28 PM, Tom Goddard via Chimera-users chimera-users@cgl.ucsf.edu wrote:
Hi Tommy,
Sure those things can be easily be done. I'd encourage you to use ChimeraX instead of the old Chimera program. Also best to email questions to the Chimera mailing list (chimera-users@cgl.ucsf.edu) or ChimeraX mailing list (chimerax-users@cgl.ucsf.edu).
To delete a domain of a protein in ChimeraX that is say residues 151 to 375 of chain B
delete /B:151-375
The command syntax would be different in Chimera. To add short linkers is more difficult and I will leave that question to Elaine to advise on the mailing list -- I am not the most knowledgable about how to do that.
Tom
On Apr 26, 2022, at 4:45 PM, Tommy Tong ttong@SDBRI.ORG wrote:
Dear Thomas, Good afternoon. How are you? My name is Tommy from San Diego Biomedical Research Institute, CA. I am new to Chimera software and my level of usage has been at the basic level, eg selecting chains and to color label the specific region on the protein.
May I ask if there is a way to selectively deleting a specific domain on a protein from a pdb file? I want to show graphically how the structure of the molecule will look like without the domain(s). In addition, is it possible to add short amino acid sequence, such as short linkers (eg GSGS) after a domain has been deleted from the protein structure?
I am currently using UCSF Chimera version 1.16.
Your help and advice are greatly appreciated. Thank you for your time.
Sincerely, Tommy
Dear Elaine, Good morning. Thank you so much for the guidance. I will try out these syntax as well as using ChimeraX. __
Sincerely, Tommy
On 4/27/22, 8:57 AM, "Elaine Meng" meng@cgl.ucsf.edu wrote:
Hi Tommy, Currently I would still use Chimera (rather than ChimeraX) for building a short linker because it has a command to add amino acids one at a time to the end of a chain.
Chimera command "addaa": https://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/addaa.html
Example to add tyrosine as residue number 30 after residue 29 at the end of chain A: addaa tyr,30 :29.A
You can also delete residues in Chimera. The analogous Chimera command to Tom's ChimeraX example is: delete :151-375.B
If you simply want to hide part of a structure, you can just hide it rather than deleting it, e.g. Chimera commands ~disp :151-375.B ~ribbon :151-375.B
However, I understand that if you wanted to append a linker you really need to delete that other part first.
This page explains how to specify models, chains, residues, atoms in the Chimera command line: https://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/frameatom_spec.html
Then if you want to join the model that has the linker with another protein opened as a separate model, see Chimera's Build Structure tool (menu: Tools... Structure Editing... Build Structure), the Join Models section. See the help: https://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/editing/editing.html https://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/editing/editing.html#join
We are just now adding join models to ChimeraX, but it does not yet have anything like addaa.
I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
> On Apr 26, 2022, at 6:28 PM, Tom Goddard via Chimera-users chimera-users@cgl.ucsf.edu wrote: > > Hi Tommy, > > Sure those things can be easily be done. I'd encourage you to use ChimeraX instead of the old Chimera program. Also best to email questions to the Chimera mailing list (chimera-users@cgl.ucsf.edu) or ChimeraX mailing list (chimerax-users@cgl.ucsf.edu). > > To delete a domain of a protein in ChimeraX that is say residues 151 to 375 of chain B > > delete /B:151-375 > > The command syntax would be different in Chimera. To add short linkers is more difficult and I will leave that question to Elaine to advise on the mailing list -- I am not the most knowledgable about how to do that. > > Tom > > >> On Apr 26, 2022, at 4:45 PM, Tommy Tong ttong@SDBRI.ORG wrote: >> >> Dear Thomas, >> Good afternoon. How are you? My name is Tommy from San Diego Biomedical Research Institute, CA. I am new to Chimera software and my level of usage has been at the basic level, eg selecting chains and to color label the specific region on the protein. >> >> May I ask if there is a way to selectively deleting a specific domain on a protein from a pdb file? I want to show graphically how the structure of the molecule will look like without the domain(s). In addition, is it possible to add short amino acid sequence, such as short linkers (eg GSGS) after a domain has been deleted from the protein structure? >> >> I am currently using UCSF Chimera version 1.16. >> >> Your help and advice are greatly appreciated. >> Thank you for your time. >> >> Sincerely, >> Tommy
Dear Tom, Good morning. Thank you so much for your reply and for the guidance. I will try the ChimeraX (got to keep up with the latest stuff). 😊
Sincerely, Tommy
From: Tom Goddard goddard@cgl.ucsf.edu Date: Tuesday, April 26, 2022 at 6:28 PM To: Tommy Tong ttong@SDBRI.ORG Cc: "chimera-users@cgl.ucsf.edu List" chimera-users@cgl.ucsf.edu Subject: Re: Help and guidance on using chimera
Hi Tommy,
Sure those things can be easily be done. I'd encourage you to use ChimeraX instead of the old Chimera program. Also best to email questions to the Chimera mailing list (chimera-users@cgl.ucsf.edumailto:chimera-users@cgl.ucsf.edu) or ChimeraX mailing list (chimerax-users@cgl.ucsf.edumailto:chimerax-users@cgl.ucsf.edu).
To delete a domain of a protein in ChimeraX that is say residues 151 to 375 of chain B
delete /B:151-375
The command syntax would be different in Chimera. To add short linkers is more difficult and I will leave that question to Elaine to advise on the mailing list -- I am not the most knowledgable about how to do that.
Tom
On Apr 26, 2022, at 4:45 PM, Tommy Tong <ttong@SDBRI.ORGmailto:ttong@SDBRI.ORG> wrote:
Dear Thomas, Good afternoon. How are you? My name is Tommy from San Diego Biomedical Research Institute, CA. I am new to Chimera software and my level of usage has been at the basic level, eg selecting chains and to color label the specific region on the protein.
May I ask if there is a way to selectively deleting a specific domain on a protein from a pdb file? I want to show graphically how the structure of the molecule will look like without the domain(s). In addition, is it possible to add short amino acid sequence, such as short linkers (eg GSGS) after a domain has been deleted from the protein structure?
I am currently using UCSF Chimera version 1.16.
Your help and advice are greatly appreciated. Thank you for your time.
Sincerely, Tommy
participants (3)
-
Elaine Meng -
Tom Goddard -
Tommy Tong