I should be able to find this but haven't looked too hard. I am interested in a salt bridge between the C-terminal carboxylate and a Lys residue in the protein. I know how to visualize the Lys side chain, and the C-terminal residue. How do I visualize the carboxylate terminus? I tried backbone only actions, but nothing worked. Thanks AGSzabo
Hi Arthur, If you are showing ribbon, it suppresses the display of backbone atoms. To enable showing both backbone atoms and ribbon at the same time for the same residue, you would need to use command “ribbackbone”. (Then you may still need to display the atoms after that.) Alternatively you can hide the ribbon for just that residue (e.g. select it and then use Actions…Ribbon… hide) and then show whatever of its atoms that you want. However, it will then be detached from the rest of the ribbon and look like it is floating. Yet another approach is to not use any ribbons for that figure. I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco On Nov 24, 2016, at 4:21 PM, A G Szabo <agszabo@bell.net> wrote:
I should be able to find this but haven’t looked too hard.
I am interested in a salt bridge between the C-terminal carboxylate and a Lys residue in the protein. I know how to visualize the Lys side chain, and the C-terminal residue.
How do I visualize the carboxylate terminus? I tried backbone only actions, but nothing worked.
Thanks
AGSzabo
Elaine Thank you will try. art -----Original Message----- From: Elaine Meng [mailto:meng@cgl.ucsf.edu] Sent: November-25-16 11:24 AM To: A G Szabo Cc: chimera-users@cgl.ucsf.edu Subject: Re: [Chimera-users] simple question Hi Arthur, If you are showing ribbon, it suppresses the display of backbone atoms. To enable showing both backbone atoms and ribbon at the same time for the same residue, you would need to use command "ribbackbone". (Then you may still need to display the atoms after that.) Alternatively you can hide the ribbon for just that residue (e.g. select it and then use Actions.Ribbon. hide) and then show whatever of its atoms that you want. However, it will then be detached from the rest of the ribbon and look like it is floating. Yet another approach is to not use any ribbons for that figure. I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco On Nov 24, 2016, at 4:21 PM, A G Szabo <agszabo@bell.net> wrote:
I should be able to find this but haven't looked too hard.
I am interested in a salt bridge between the C-terminal carboxylate and a Lys residue in the protein. I know how to visualize the Lys side chain, and the C-terminal residue.
How do I visualize the carboxylate terminus? I tried backbone only actions, but nothing worked.
Thanks
AGSzabo
Elaine Thanks for trying to help. I looked at the command ribbackbone atom-spec but because I rarely use the command line I am not very familiar with what some of the designations mean. I have a C-terminal Alanine, residue 42, in the chain C #0.8. Using the menu method I was able to visualize the C-terminal carboxyl and the Ala side chains. But as you indicated this seems to float from the backbone. The bond between the N in Ala backbone is not connected to residue 41, there is a small space. So my main question is what are the parameters that I should use with the command "ribbackbone"? Thank you Arthur -----Original Message----- From: Elaine Meng [mailto:meng@cgl.ucsf.edu] Sent: November-25-16 11:24 AM To: A G Szabo Cc: chimera-users@cgl.ucsf.edu Subject: Re: [Chimera-users] simple question Hi Arthur, If you are showing ribbon, it suppresses the display of backbone atoms. To enable showing both backbone atoms and ribbon at the same time for the same residue, you would need to use command "ribbackbone". (Then you may still need to display the atoms after that.) Alternatively you can hide the ribbon for just that residue (e.g. select it and then use Actions.Ribbon. hide) and then show whatever of its atoms that you want. However, it will then be detached from the rest of the ribbon and look like it is floating. Yet another approach is to not use any ribbons for that figure. I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco On Nov 24, 2016, at 4:21 PM, A G Szabo <agszabo@bell.net> wrote:
I should be able to find this but haven't looked too hard.
I am interested in a salt bridge between the C-terminal carboxylate and a Lys residue in the protein. I know how to visualize the Lys side chain, and the C-terminal residue.
How do I visualize the carboxylate terminus? I tried backbone only actions, but nothing worked.
Thanks
AGSzabo
Hi Arthur, Sorry I was not clear. You do not need to enter any parameters, only the single-word command: ribbackbone However, the atoms may still be floating away from the ribbon, because the ribbon path is smoothed and may not pass exactly through the real atom positions. If that is the case, and it is not acceptable for your figure, some other possibilities are: (A) Do not try to combine backbone atoms and ribbons for this image. Just show backbone atoms, no ribbons at all (even for other residues). (B) Try an unsmoothed ribbon, for example command: ribspline cardinal -OR- ribspline cardinal smooth strand … the latter providing some compromise smoothing of beta-strands. However, this ribbon is not as pretty in some places as the smoothed default ribbon and the relationship to the atoms may still look weird, especially at the termini. I tried one example at the C-terminus of a protein and noticed it it was better with cardinal spline to hide the ribbon for just that residue, in my case residue 309 of chain A and also hide its N atom: ~ribb :309.A disp :309.A ~disp :309.A@N If you want, you can go back to the default smoothed ribbon path with command: ribspline b I hope this helps. Given the limitations of the program, you still might not be able to achieve the appearance you wanted, however. Elaine ----- Elaine C. Meng, Ph.D. UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco On Nov 25, 2016, at 11:52 AM, A G Szabo <agszabo@bell.net> wrote:
Elaine
Thanks for trying to help.
I looked at the command
ribbackbone atom-spec
but because I rarely use the command line I am not very familiar with what some of the designations mean.
I have a C-terminal Alanine, residue 42, in the chain C #0.8.
Using the menu method I was able to visualize the C-terminal carboxyl and the Ala side chains. But as you indicated this seems to float from the backbone. The bond between the N in Ala backbone is not connected to residue 41, there is a small space.
So my main question is what are the parameters that I should use with the command "ribbackbone"?
Thank you
Arthur
-----Original Message----- From: Elaine Meng [mailto:meng@cgl.ucsf.edu] Sent: November-25-16 11:24 AM To: A G Szabo Cc: chimera-users@cgl.ucsf.edu Subject: Re: [Chimera-users] simple question
Hi Arthur, If you are showing ribbon, it suppresses the display of backbone atoms. To enable showing both backbone atoms and ribbon at the same time for the same residue, you would need to use command "ribbackbone". (Then you may still need to display the atoms after that.) Alternatively you can hide the ribbon for just that residue (e.g. select it and then use Actions.Ribbon. hide) and then show whatever of its atoms that you want. However, it will then be detached from the rest of the ribbon and look like it is floating. Yet another approach is to not use any ribbons for that figure. I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco
On Nov 24, 2016, at 4:21 PM, A G Szabo <agszabo@bell.net> wrote:
I should be able to find this but haven't looked too hard.
I am interested in a salt bridge between the C-terminal carboxylate and a Lys residue in the protein. I know how to visualize the Lys side chain, and the C-terminal residue.
How do I visualize the carboxylate terminus? I tried backbone only actions, but nothing worked.
Thanks
AGSzabo
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On Nov 25, 2016, at 12:49 PM, Elaine Meng <meng@cgl.ucsf.edu> wrote:
You do not need to enter any parameters, only the single-word command:
ribbackbone
… although you can specify a specific model, for example: ribbackbone #0.8 I prefer commands, but maybe you would prefer to use the Selection Inspector dialog. If you have something selected (atom, bond, whatever) you can then choose "Actions… Inspect” in the menu or click the green magnifying glass near the bottom right corner of the Chimera window to show the Selection Inspector. Then, you can Inspect: Atom, or (if you have any bonds selected) Bond, or Molecule model. Even if you only have a small part like one atom or bond selected, you can still use this dialog to inspect “Residue” or “Molecule model” and change its settings. For example, in Inspect: Molecule model, there is “ribbon hides backbone atoms” true or false, and “ribbon spline” settings. The main thing is that some settings are for the atom, some for the residue, some for the whole model only so you might have to look in all those sections to find the setting you are interested in changing. Best, Elaine
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