Hi Maja, I still can't tell for certain what you were doing wrong for join peptide since your session did not have the two atoms selected. However, I'm guessing these were some of the problems: (1) ribbon is displayed, which by default hides the backbone atoms. So I think you were probably selecting sidechain atoms. In one model, the C-terminal asparagine has an amide sidechain and probably you were selecting the C in the sidechain. To see the backbone atoms you would either need to hide ribbon or use "cartoon suppress false" to enable showing both the ribbon and the backbone atoms at the same time. (2) In the other model, although you can see a proline N (since it is both sidechain and backbone), that proline is not the N-terminal residue of the model. There is a dashed line for missing peptide coordinates and the proline is actually in the middle of the chain. The N-terminal residue of that model is actually a methionine that is far away on the other side of the structure. I will respond privately to you with some screenshots that may help to clarify these issues. Best, 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 Mar 7, 2024, at 12:27 AM, Maja Divjak via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:
Hi Elaine,
Thanks so much for this kind offer. I have sent to you by SFT, as the file is rather large.
Thanks so much and best wishes,
Maja
-----Original Message----- From: Elaine Meng <meng@cgl.ucsf.edu> Sent: Thursday, 7 March 2024 4:09 AM To: Maja Divjak <Maja.Divjak@petermac.org> Cc: ChimeraX Users Help <chimerax-users@cgl.ucsf.edu> Subject: Re: [chimerax-users] Trying to join two structures unsuccessfully
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Hi Maja, We can't tell what the problem is with join models in your case without your specific data, e.g. a session with the two atoms selected (the N at the N-term of one peptide in one model and the C at the C-term of the other peptide in the other model). If you don't mind sharing it you could try using Help... Report a Bug and attaching a session file, but if it needs to be kept private you could send it to just me. Elaine
On Mar 6, 2024, at 12:43 AM, Maja Divjak via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:
Hi Elaine,
Hope you're well! After getting tug to work successfully, I'm still having trouble joining the ends, even though they are now nice and close together and are in separate models. I've been using the 'join models' peptide bond option you referred to below, but it's still giving me errors about not having a C selected when I clearly do. This happens when trying to select a C at either end. I've updated to ChimeraX 1.7.1, but this didn't help. Weird. I'll fiddle with this a bit more tomorrow and try to sort it out in my animation software if I can't get it to work. The major problem has been the tug, which is now working.
Thanks so much and best wishes,
Maja
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