Trying to join two structures unsuccessfully
Hi there, Hope you're well. I am trying to join the two structures as shown in the image attached. I would like to join the disordered chain shown in green to the purple chain and the residues I would like to join are highlighted. I would like the green disordered chain to be dragged over to join the purple structure without moving any of the ordered domains that are linked to it (orange). I have tried selecting individual atoms ie N and C atoms from these residues (as shown) and using the command tools > structure editing > build structure > join models from the drop down menu. I adjusted C-N length to 1.6 and set to 'move atoms in larger model', thinking this would move the green chain. Hitting apply gives me the error dialogue 'No atoms selected'. I also tried Adjust Bonds > with options for Delete selected bonds > and add reasonable. There are no error messages, but the log says that no bonds were created. Not sure what I'm doing wrong or what the correct process is for joining models in this way please? Is this even possible? Clearly I'm not selecting the atoms appropriately. I am using Chimera X version 1.6.1 Thanks so much and best wishes, Maja Dr Maja Divjak BAppSc(Hons), PhD, Grad Cert 3D Animation (AFTRS) Biomedical Animator Office of Cancer Research [Description: cid:image001.jpg@01D35ECE.31407C60]
Dear Maja, Apologies if you are getting multiple copies of this answer from me. I keep getting error messages that my reply could not be sent to the list! So, here is my third try. If you've been getting my previous messages (even though I don't think the rest of the list is), please ignore and pardon me for the spam! Adding a bond only works when the atoms are in the same model as each other (typically a structure opened from one PDB file is one model). Also simply adding a bond won't move anything. It will just make a long bond between the atoms in their current positions, or if you choose "reasonable" only, it won't add any bond because the bond would be too long to be reasonable. <https://rbvi.ucsf.edu/chimerax/docs/user/tools/buildstructure.html#bonds> You can see what model(s) you have by looking in the Model Panel: <https://rbvi.ucsf.edu/chimerax/docs/user/tools/modelpanel.html> If the two atoms are in two different models (typically opened from two different input files), the "join models" Peptide Bond option should work if you really have exactly two atoms selected, the peptide terminal "N" in one model and the peptide terminal "C" in the other model. As far as I can tell these two are selected in your image, so I couldn't say why you get an error message. If the atoms are in the same model as each other, however, it will not work. You would need to split the model so that they are in separate models first. You can try command "info atoms sel" to list in the Log what you have selected. In my "join peptide" test case I get the following, which confirms I have the correct atoms from two different models selected: info atoms sel atom id #1/A:29@C idatm_type Cac atom id #2/A:1@N idatm_type N3+ However, join models is not going to change the conformation of the peptide, it will just move one model (e.g. the entire green one if it has more atoms than the purple one) as a rigid body to form the specified bond with the other model. <https://rbvi.ucsf.edu/chimerax/docs/user/tools/buildstructure.html#join> I hope this helps, 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
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 -----Original Message----- From: Elaine Meng <meng@cgl.ucsf.edu> Sent: Tuesday, 5 March 2024 11:33 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 ! EXTERNAL EMAIL: Think before you click. If suspicious send to CyberReport@petermac.org Dear Maja, Apologies if you are getting multiple copies of this answer from me. I keep getting error messages that my reply could not be sent to the list! So, here is my third try. If you've been getting my previous messages (even though I don't think the rest of the list is), please ignore and pardon me for the spam! Adding a bond only works when the atoms are in the same model as each other (typically a structure opened from one PDB file is one model). Also simply adding a bond won't move anything. It will just make a long bond between the atoms in their current positions, or if you choose "reasonable" only, it won't add any bond because the bond would be too long to be reasonable. <https://rbvi.ucsf.edu/chimerax/docs/user/tools/buildstructure.html#bonds> You can see what model(s) you have by looking in the Model Panel: <https://rbvi.ucsf.edu/chimerax/docs/user/tools/modelpanel.html> If the two atoms are in two different models (typically opened from two different input files), the "join models" Peptide Bond option should work if you really have exactly two atoms selected, the peptide terminal "N" in one model and the peptide terminal "C" in the other model. As far as I can tell these two are selected in your image, so I couldn't say why you get an error message. If the atoms are in the same model as each other, however, it will not work. You would need to split the model so that they are in separate models first. You can try command "info atoms sel" to list in the Log what you have selected. In my "join peptide" test case I get the following, which confirms I have the correct atoms from two different models selected: info atoms sel atom id #1/A:29@C idatm_type Cac atom id #2/A:1@N idatm_type N3+ However, join models is not going to change the conformation of the peptide, it will just move one model (e.g. the entire green one if it has more atoms than the purple one) as a rigid body to form the specified bond with the other model. <https://rbvi.ucsf.edu/chimerax/docs/user/tools/buildstructure.html#join> I hope this helps, 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
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
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 ! EXTERNAL EMAIL: Think before you click. If suspicious send to CyberReport@petermac.org 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
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
! EXTERNAL EMAIL: Think before you click. If suspicious send to CyberReport@petermac.org
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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participants (2)
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Elaine Meng -
Maja Divjak