displaying ribbon and tube simultaneously
Hi, I would like to display a model as a ribbon, but then specify a single helix to show as a tube. So far I’ve only been able to show the model either entirely as a ribbon, or entirely as tubes. Is there syntax I can use to blend the two helix styles? Thanks, Joel
Hi Joel, Currently an atomic structure in ChimeraX has one setting for whether tube helices are shown, so it applies to all helices in the structure. The docs for the "cartoon style" command suggest this but could say it more directly https://www.rbvi.ucsf.edu/chimerax/docs/user/commands/cartoon.html#style <https://www.rbvi.ucsf.edu/chimerax/docs/user/commands/cartoon.html#style> Of course you can get your way with more trouble by opening two copies of the structure and shown the one tube helix using one copy, and the normal ribbon for the other copy with the helix that is a tube not displayed. The reason we don't give tube style control over each helix is it complicates the code and we already have vastly more features we would like in ChimeraX than we have time to work on. Tom
On Apr 23, 2020, at 9:59 AM, Joel Meyerson <jrm2008@med.cornell.edu> wrote:
Hi, I would like to display a model as a ribbon, but then specify a single helix to show as a tube. So far I’ve only been able to show the model either entirely as a ribbon, or entirely as tubes. Is there syntax I can use to blend the two helix styles?
Thanks, Joel _______________________________________________ ChimeraX-users mailing list ChimeraX-users@cgl.ucsf.edu <mailto:ChimeraX-users@cgl.ucsf.edu> Manage subscription: http://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users <http://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users>
Hi Joel, Not really, with details below. The "cartoon style" settings are per-model, disallowing two different styles in the same model. <http://rbvi.ucsf.edu/chimerax/docs/user/commands/cartoon.html#subcommands> I was hoping I could simply open two copies and show the complementary residue ranges in the different styles, hiding the rest of the cartoon in each. Unfortunately the ends don't join smoothly. You could try to fudge it with showing an additional residue of overlap and/or making the tube fat and/or viewing from a strategic angle, but it may not look very good. It was fairly ugly in my experiments. Although both models' cartoon paths pass through the CA positions exactly, you can't turn off display precisely at the CA, but only the cartoon segment per residue, which has the CA in the middle, not the end. I also tried 100% transparency in case that was any different than simply hiding the cartoon of some residues, but it gave the same result. The least bad, at least in my couple of test cases, was to show helix range + 1 on each end in the tube model, and all but the helix range in the ribbon model. Attached images of (1) that (tube has helix +1 on each end), (2) completely disjoint, complementary ranges displayed (3) more of the ribbon model shown so you can see how the paths diverge. We plan to eventually add helix axis calculations that would display a straight cylinder. Maybe that would better accomplish your goal. Currently available alternatives include just creating a straight cylinder as an object with BILD format or as a surface model with the recently added "shape" command, but it may be difficult to get the dimensions and placement just right. <http://rbvi.ucsf.edu/chimerax/docs/user/commands/shape.html> <http://rbvi.ucsf.edu/chimerax/docs/user/formats/bild.html> I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Apr 23, 2020, at 9:59 AM, Joel Meyerson <jrm2008@med.cornell.edu> wrote:
Hi, I would like to display a model as a ribbon, but then specify a single helix to show as a tube. So far I’ve only been able to show the model either entirely as a ribbon, or entirely as tubes. Is there syntax I can use to blend the two helix styles?
Thanks, Joel
Hi Joel, If you try to use the trick of two copies of the structure I see from Elaine's picture that the two copies don't join very well. I would suspect that if you include a much longer stretch (10 residues) of the tube helix model beyond the ends of the tube then the match of the ends to the copy without the tubes will become better. It is just a theory. The tube style changes the spline that the ribbon passes through but the effects of the change in spline shape caused by the tube should fall off if you move many residues away from the tube helix ends. I have not tried it. Tom
On Apr 23, 2020, at 10:48 AM, Elaine Meng <meng@cgl.ucsf.edu> wrote:
Hi Joel, Not really, with details below. The "cartoon style" settings are per-model, disallowing two different styles in the same model. <http://rbvi.ucsf.edu/chimerax/docs/user/commands/cartoon.html#subcommands <http://rbvi.ucsf.edu/chimerax/docs/user/commands/cartoon.html#subcommands>>
I was hoping I could simply open two copies and show the complementary residue ranges in the different styles, hiding the rest of the cartoon in each. Unfortunately the ends don't join smoothly. You could try to fudge it with showing an additional residue of overlap and/or making the tube fat and/or viewing from a strategic angle, but it may not look very good. It was fairly ugly in my experiments.
Although both models' cartoon paths pass through the CA positions exactly, you can't turn off display precisely at the CA, but only the cartoon segment per residue, which has the CA in the middle, not the end.
I also tried 100% transparency in case that was any different than simply hiding the cartoon of some residues, but it gave the same result.
The least bad, at least in my couple of test cases, was to show helix range + 1 on each end in the tube model, and all but the helix range in the ribbon model. Attached images of (1) that (tube has helix +1 on each end), (2) completely disjoint, complementary ranges displayed (3) more of the ribbon model shown so you can see how the paths diverge.
We plan to eventually add helix axis calculations that would display a straight cylinder. Maybe that would better accomplish your goal. Currently available alternatives include just creating a straight cylinder as an object with BILD format or as a surface model with the recently added "shape" command, but it may be difficult to get the dimensions and placement just right.
<http://rbvi.ucsf.edu/chimerax/docs/user/commands/shape.html <http://rbvi.ucsf.edu/chimerax/docs/user/commands/shape.html>> <http://rbvi.ucsf.edu/chimerax/docs/user/formats/bild.html <http://rbvi.ucsf.edu/chimerax/docs/user/formats/bild.html>>
I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
<plus1.png><disjoint.png><allribbon.png>
On Apr 23, 2020, at 9:59 AM, Joel Meyerson <jrm2008@med.cornell.edu <mailto:jrm2008@med.cornell.edu>> wrote:
Hi, I would like to display a model as a ribbon, but then specify a single helix to show as a tube. So far I’ve only been able to show the model either entirely as a ribbon, or entirely as tubes. Is there syntax I can use to blend the two helix styles?
Thanks, Joel
_______________________________________________ ChimeraX-users mailing list ChimeraX-users@cgl.ucsf.edu Manage subscription: http://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users
Thanks Tom, that does look better. Here is an example of showing helix +2 on each end in the tube model and hiding all but those same residues (helix +2 on each end) in the ribbon model. I just didn't try long enough nubbins before. Just 2 seems to be enough in this case: 2gbp helix containing residues 152-169. For the following example commands, the model already displayed with tube helices is #2,and the one with regular ribbons #1. ~cartoon cartoon #1:130-180 [... that was just to show a longer stretch without showing the entire protein which would be too busy...] cartoon #2:150-171 ~cartoon #1:150-171
On Apr 23, 2020, at 11:05 AM, Tom Goddard <goddard@sonic.net> wrote:
Hi Joel,
If you try to use the trick of two copies of the structure I see from Elaine's picture that the two copies don't join very well. I would suspect that if you include a much longer stretch (10 residues) of the tube helix model beyond the ends of the tube then the match of the ends to the copy without the tubes will become better. It is just a theory. The tube style changes the spline that the ribbon passes through but the effects of the change in spline shape caused by the tube should fall off if you move many residues away from the tube helix ends. I have not tried it.
Tom
On Apr 23, 2020, at 10:48 AM, Elaine Meng <meng@cgl.ucsf.edu> wrote:
Hi Joel, Not really, with details below. The "cartoon style" settings are per-model, disallowing two different styles in the same model. <http://rbvi.ucsf.edu/chimerax/docs/user/commands/cartoon.html#subcommands>
I was hoping I could simply open two copies and show the complementary residue ranges in the different styles, hiding the rest of the cartoon in each. Unfortunately the ends don't join smoothly. You could try to fudge it with showing an additional residue of overlap and/or making the tube fat and/or viewing from a strategic angle, but it may not look very good. It was fairly ugly in my experiments.
Although both models' cartoon paths pass through the CA positions exactly, you can't turn off display precisely at the CA, but only the cartoon segment per residue, which has the CA in the middle, not the end.
I also tried 100% transparency in case that was any different than simply hiding the cartoon of some residues, but it gave the same result.
The least bad, at least in my couple of test cases, was to show helix range + 1 on each end in the tube model, and all but the helix range in the ribbon model. Attached images of (1) that (tube has helix +1 on each end), (2) completely disjoint, complementary ranges displayed (3) more of the ribbon model shown so you can see how the paths diverge.
We plan to eventually add helix axis calculations that would display a straight cylinder. Maybe that would better accomplish your goal. Currently available alternatives include just creating a straight cylinder as an object with BILD format or as a surface model with the recently added "shape" command, but it may be difficult to get the dimensions and placement just right.
<http://rbvi.ucsf.edu/chimerax/docs/user/commands/shape.html> <http://rbvi.ucsf.edu/chimerax/docs/user/formats/bild.html>
I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
<plus1.png><disjoint.png><allribbon.png>
On Apr 23, 2020, at 9:59 AM, Joel Meyerson <jrm2008@med.cornell.edu> wrote:
Hi, I would like to display a model as a ribbon, but then specify a single helix to show as a tube. So far I’ve only been able to show the model either entirely as a ribbon, or entirely as tubes. Is there syntax I can use to blend the two helix styles?
Thanks, Joel
Hi Elaine and Tom, Thanks for the answer and the helpful tips. That does indeed look like a nice way to achieve the desired effect. I’ll do that. All the best, Joel From: Elaine Meng <meng@cgl.ucsf.edu> Reply-To: ChimeraX Users Help <chimerax-users@cgl.ucsf.edu> Date: Thursday, April 23, 2020 at 1:19 PM To: ChimeraX Users Help <chimerax-users@cgl.ucsf.edu>, Joel Meyerson <jrm2008@med.cornell.edu> Subject: [EXTERNAL] Re: [chimerax-users] displaying ribbon and tube simultaneously Thanks Tom, that does look better. Here is an example of showing helix +2 on each end in the tube model and hiding all but those same residues (helix +2 on each end) in the ribbon model. I just didn't try long enough nubbins before. Just 2 seems to be enough in this case: 2gbp helix containing residues 152-169. For the following example commands, the model already displayed with tube helices is #2,and the one with regular ribbons #1. ~cartoon cartoon #1:130-180 [... that was just to show a longer stretch without showing the entire protein which would be too busy...] cartoon #2:150-171 ~cartoon #1:150-171 [cid:image001.png@01D6197E.3BE42730] On Apr 23, 2020, at 11:05 AM, Tom Goddard <goddard@sonic.net<mailto:goddard@sonic.net>> wrote: Hi Joel, If you try to use the trick of two copies of the structure I see from Elaine's picture that the two copies don't join very well. I would suspect that if you include a much longer stretch (10 residues) of the tube helix model beyond the ends of the tube then the match of the ends to the copy without the tubes will become better. It is just a theory. The tube style changes the spline that the ribbon passes through but the effects of the change in spline shape caused by the tube should fall off if you move many residues away from the tube helix ends. I have not tried it. Tom On Apr 23, 2020, at 10:48 AM, Elaine Meng <meng@cgl.ucsf.edu<mailto:meng@cgl.ucsf.edu>> wrote: Hi Joel, Not really, with details below. The "cartoon style" settings are per-model, disallowing two different styles in the same model. <http://rbvi.ucsf.edu/chimerax/docs/user/commands/cartoon.html#subcommands> I was hoping I could simply open two copies and show the complementary residue ranges in the different styles, hiding the rest of the cartoon in each. Unfortunately the ends don't join smoothly. You could try to fudge it with showing an additional residue of overlap and/or making the tube fat and/or viewing from a strategic angle, but it may not look very good. It was fairly ugly in my experiments. Although both models' cartoon paths pass through the CA positions exactly, you can't turn off display precisely at the CA, but only the cartoon segment per residue, which has the CA in the middle, not the end. I also tried 100% transparency in case that was any different than simply hiding the cartoon of some residues, but it gave the same result. The least bad, at least in my couple of test cases, was to show helix range + 1 on each end in the tube model, and all but the helix range in the ribbon model. Attached images of (1) that (tube has helix +1 on each end), (2) completely disjoint, complementary ranges displayed (3) more of the ribbon model shown so you can see how the paths diverge. We plan to eventually add helix axis calculations that would display a straight cylinder. Maybe that would better accomplish your goal. Currently available alternatives include just creating a straight cylinder as an object with BILD format or as a surface model with the recently added "shape" command, but it may be difficult to get the dimensions and placement just right. <http://rbvi.ucsf.edu/chimerax/docs/user/commands/shape.html> <http://rbvi.ucsf.edu/chimerax/docs/user/formats/bild.html> I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco <plus1.png><disjoint.png><allribbon.png> On Apr 23, 2020, at 9:59 AM, Joel Meyerson <jrm2008@med.cornell.edu> wrote: Hi, I would like to display a model as a ribbon, but then specify a single helix to show as a tube. So far I’ve only been able to show the model either entirely as a ribbon, or entirely as tubes. Is there syntax I can use to blend the two helix styles? Thanks, Joel
participants (3)
-
Elaine Meng -
Joel Meyerson -
Tom Goddard