[Chimera-users] Creating new models from existing crystal structures
meng at cgl.ucsf.edu
Mon Feb 8 15:10:07 PST 2021
You're welcome, I'm glad you figured it out!
> On Feb 8, 2021, at 2:40 PM, Moradkhan, Tiglath A <tmoradkhan at csus.edu> wrote:
> Hi Elaine
> Nevermind, I found my error. I tested the Join Model tool with 1AV1 which has four chains and I was able to correctly pick the correct C and N atoms to join residue segments from each chain. The select command that I had written originally wasn't right so it was picking the correct atoms to join.
> Thanks for your help.
> > On Feb 8, 2021, at 2:27 PM, Elaine Meng <meng at cgl.ucsf.edu> wrote:
> > If the residue is already in a peptide bond, you can't add another peptide bond. You would have to delete the rest of the chain after 130 in one copy of the model and the rest of the chain before 131 in the other copy for it to make sense.
> > Also, make sure that your "select" command is selecting exactly two atoms, 1 from each model.
> > Elaine
> >> On Feb 8, 2021, at 1:53 PM, Moradkhan, Tiglath A <tmoradkhan at csus.edu> wrote:
> >> Hi Elaine
> >> I've been using the biological assembly of 3R2P and I'm thinking that the reason why it's not working is because both chains are labeled A. I'm just following a paper where they're building a monomeric structure using the residue fragments but in their case the biological assembly of 3R2P is labeled as chain A and chain B.
> >> From: Elaine Meng <meng at cgl.ucsf.edu>
> >> Sent: Monday, February 8, 2021 1:01 PM
> >> To: Moradkhan, Tiglath A <tmoradkhan at csus.edu>
> >> Cc: chimera-users at cgl.ucsf.edu <chimera-users at cgl.ucsf.edu>
> >> Subject: Re: [Chimera-users] Creating new models from existing crystal structures
> >> Hi Tiglath,
> >> If you just opened 3r2p one time, you only have one model. Join works on bonding two separate models. Also it contains only chain A (there is no chain B in this structure) and residue 130 in chain A is already bonded to residue 131 in chain A. So I do not understand what you already did to modify the structure(s) before joining, or what you are trying to do now, sorry.
> >> You could send a session file if you want.
> >> Elaine
> >> -----
> >> Elaine C. Meng, Ph.D.
> >> UCSF Chimera(X) team
> >> Department of Pharmaceutical Chemistry
> >> University of California, San Francisco
> >>> On Feb 8, 2021, at 12:35 PM, Moradkhan, Tiglath A <tmoradkhan at csus.edu> wrote:
> >>> Hi
> >>> I'm trying to join two models together using the Build Structure tool but I'm having problems. Here is my process.
> >>> • Using the 3R2P crystal structure I select residues 3-130 from chain A and 131-182 from chain B
> >>> • Then using the following command in Chimera I select the N atom of residue 130 that will form a bond with the C atom of residue 131: sel #0:130 at N#1:131 at C (#0 is the name of the 3-130 segment and #1 is the name of the 131-182 segment)
> >>> • Then using the Build Structure tool I select Form C-N peptide bond, but the Apply button doesn't activate.
> >>> I don't understand what the issue is. Is the command that I've written wrong?
> >>> I would be very glad for your help. I can provide the pdb files of the residue segments if necessary.
> >>> Thanks
> >>> Tiglath
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