Hi Elaine, when coloring a helix differently from the attached coils, is there a means to prevent the first short segment of the coil to get the color of the helix? It seems to me there was some kind of "halfbond"-mode one... Best, Xavier
Hi Xavier, In ChimeraX the ribbon shape changes at the CA atom, but the ribbon color changes at the peptide bond; I believe some other programs also do it this way. In Chimera, however, this is not an issue: the color changes at the same place that the ribbon shape changes, at the peptide bond.
See attached screenshot with Chimera image on top, ChimeraX below.
However, there is a partial solution. There is a currently undocumented option in "cartoon style" ... it is "ssEnds long" (default "ssEnds short"). However, this only extends the shape to the peptide bond at the C-terminal end of each helix and strand. There were technical reasons that it did not work for the N-terminal ends, so the option is not very satisfying and that is one reason it is not described in the help page currently. However, you can try
cartoon style ssEnds long
and see if that is good enough for you. Best, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
In ChimeraX after "cartoon style ssEnds long" the helix shape extends to the peptide bond on the right (C-term end of helix) but not the N-term peptide bond on teh left:
On Nov 29, 2022, at 6:57 AM, F.Xavier Gomis-Rüth via ChimeraX-users chimerax-users@cgl.ucsf.edu wrote:
Hi Elaine, when coloring a helix differently from the attached coils, is there a means to prevent the first short segment of the coil to get the color of the helix? It seems to me there was some kind of "halfbond"-mode one... Best, Xavier -- <fxgr_signanew.jpg> _______________________________________________ ChimeraX-users mailing list ChimeraX-users@cgl.ucsf.edu Manage subscription: https://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users
Dear Elaine, thanks a lot for pointing this out, it is, as you state, a good solution however partial. If this is not an issue in old Chimera, it may be implemented at some point in ChimeraX. In the meantime, I will have to go back to the old program. Best, Xavier
On 29/11/22 18:20, Elaine Meng wrote:
Hi Xavier, In ChimeraX the ribbon shape changes at the CA atom, but the ribbon color changes at the peptide bond; I believe some other programs also do it this way. In Chimera, however, this is not an issue: the color changes at the same place that the ribbon shape changes, at the peptide bond.
See attached screenshot with Chimera image on top, ChimeraX below.
However, there is a partial solution. There is a currently undocumented option in "cartoon style" ... it is "ssEnds long" (default "ssEnds short"). However, this only extends the shape to the peptide bond at the C-terminal end of each helix and strand. There were technical reasons that it did not work for the N-terminal ends, so the option is not very satisfying and that is one reason it is not described in the help page currently. However, you can try
cartoon style ssEnds long
and see if that is good enough for you. Best, Elaine
Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
In ChimeraX after "cartoon style ssEnds long" the helix shape extends to the peptide bond on the right (C-term end of helix) but not the N-term peptide bond on teh left:
On Nov 29, 2022, at 6:57 AM, F.Xavier Gomis-Rüth via ChimeraX-users chimerax-users@cgl.ucsf.edu wrote:
Hi Elaine, when coloring a helix differently from the attached coils, is there a means to prevent the first short segment of the coil to get the color of the helix? It seems to me there was some kind of "halfbond"-mode one... Best, Xavier -- <fxgr_signanew.jpg> _______________________________________________ ChimeraX-users mailing list ChimeraX-users@cgl.ucsf.edu Manage subscription: https://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users
HI Xavier, The ribbon calculation is completely different in ChimeraX than in Chimera, so my guess is that this part of ChimeraX is unlikely to change. I thought other programs (Pymol maybe?) also have the coloring that extends beyond the wide part of the ribbons, like ChimeraX, but I understand one may prefer the cleaner look in Chimera. Personally I don't notice it often because I usually don't color coil differently than helix/strand. Best, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Nov 30, 2022, at 2:16 AM, F.Xavier Gomis-Rüth via ChimeraX-users chimerax-users@cgl.ucsf.edu wrote:
Dear Elaine, thanks a lot for pointing this out, it is, as you state, a good solution however partial. If this is not an issue in old Chimera, it may be implemented at some point in ChimeraX. In the meantime, I will have to go back to the old program. Best, Xavier
On 29/11/22 18:20, Elaine Meng wrote:
Hi Xavier, In ChimeraX the ribbon shape changes at the CA atom, but the ribbon color changes at the peptide bond; I believe some other programs also do it this way. In Chimera, however, this is not an issue: the color changes at the same place that the ribbon shape changes, at the peptide bond.
See attached screenshot with Chimera image on top, ChimeraX below.
However, there is a partial solution. There is a currently undocumented option in "cartoon style" ... it is "ssEnds long" (default "ssEnds short"). However, this only extends the shape to the peptide bond at the C-terminal end of each helix and strand. There were technical reasons that it did not work for the N-terminal ends, so the option is not very satisfying and that is one reason it is not described in the help page currently. However, you can try
cartoon style ssEnds long
and see if that is good enough for you. Best, Elaine
Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
<Screen Shot 2022-11-29 at 8.50.24 AM.png>
In ChimeraX after "cartoon style ssEnds long" the helix shape extends to the peptide bond on the right (C-term end of helix) but not the N-term peptide bond on teh left: <Screen Shot 2022-11-29 at 9.18.18 AM.png>
On Nov 29, 2022, at 6:57 AM, F.Xavier Gomis-Rüth via ChimeraX-users chimerax-users@cgl.ucsf.edu wrote:
Hi Elaine, when coloring a helix differently from the attached coils, is there a means to prevent the first short segment of the coil to get the color of the helix? It seems to me there was some kind of "halfbond"-mode one... Best, Xavier -- <fxgr_signanew.jpg> _______________________________________________ ChimeraX-users mailing list ChimeraX-users@cgl.ucsf.edu Manage subscription: https://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users
-- <fxgr_signanew.jpg> _______________________________________________ ChimeraX-users mailing list ChimeraX-users@cgl.ucsf.edu Manage subscription: https://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users
Ok, thanks for the info. I will have to keep a functioning version of old Chimera then. Best, Xavier
On 30/11/22 16:52, Elaine Meng wrote:
HI Xavier, The ribbon calculation is completely different in ChimeraX than in Chimera, so my guess is that this part of ChimeraX is unlikely to change. I thought other programs (Pymol maybe?) also have the coloring that extends beyond the wide part of the ribbons, like ChimeraX, but I understand one may prefer the cleaner look in Chimera. Personally I don't notice it often because I usually don't color coil differently than helix/strand. Best, Elaine
Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Nov 30, 2022, at 2:16 AM, F.Xavier Gomis-Rüth via ChimeraX-userschimerax-users@cgl.ucsf.edu wrote:
Dear Elaine, thanks a lot for pointing this out, it is, as you state, a good solution however partial. If this is not an issue in old Chimera, it may be implemented at some point in ChimeraX. In the meantime, I will have to go back to the old program. Best, Xavier
On 29/11/22 18:20, Elaine Meng wrote:
Hi Xavier, In ChimeraX the ribbon shape changes at the CA atom, but the ribbon color changes at the peptide bond; I believe some other programs also do it this way. In Chimera, however, this is not an issue: the color changes at the same place that the ribbon shape changes, at the peptide bond.
See attached screenshot with Chimera image on top, ChimeraX below.
However, there is a partial solution. There is a currently undocumented option in "cartoon style" ... it is "ssEnds long" (default "ssEnds short"). However, this only extends the shape to the peptide bond at the C-terminal end of each helix and strand. There were technical reasons that it did not work for the N-terminal ends, so the option is not very satisfying and that is one reason it is not described in the help page currently. However, you can try
cartoon style ssEnds long
and see if that is good enough for you. Best, Elaine
Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
<Screen Shot 2022-11-29 at 8.50.24 AM.png>
In ChimeraX after "cartoon style ssEnds long" the helix shape extends to the peptide bond on the right (C-term end of helix) but not the N-term peptide bond on teh left: <Screen Shot 2022-11-29 at 9.18.18 AM.png>
On Nov 29, 2022, at 6:57 AM, F.Xavier Gomis-Rüth via ChimeraX-userschimerax-users@cgl.ucsf.edu wrote:
Hi Elaine, when coloring a helix differently from the attached coils, is there a means to prevent the first short segment of the coil to get the color of the helix? It seems to me there was some kind of "halfbond"-mode one... Best, Xavier -- <fxgr_signanew.jpg> _______________________________________________ ChimeraX-users mailing list ChimeraX-users@cgl.ucsf.edu Manage subscription: https://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users
-- <fxgr_signanew.jpg> _______________________________________________ ChimeraX-users mailing list ChimeraX-users@cgl.ucsf.edu Manage subscription: https://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users
participants (2)
-
Elaine Meng -
F.Xavier Gomis-Rüth