[Chimera-users] Help and guidance on using chimera

[Tommy Tong]

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 at cgl.ucsf.edu>
Date: Tuesday, April 26, 2022 at 6:28 PM
To: Tommy Tong <ttong at SDBRI.ORG>
Cc: "chimera-users at cgl.ucsf.edu List" <chimera-users at 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 at cgl.ucsf.edu<mailto:chimera-users at cgl.ucsf.edu>) or ChimeraX mailing list (chimerax-users at cgl.ucsf.edu<mailto:chimerax-users at 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 at SDBRI.ORG<mailto:ttong at 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

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