Re: [Chimera-users] A specific request for visualizing a model in Chimera
Hi Qian, I don't know of any way to "smooth" those junctions between coil and helix/strand, but I believe that many people 3D print the ribbons and they have not been a problem as long as you make the overall ribbon thick enough, e.g. with the "struts" command or Ribbon Style Editor.
https://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/struts.html https://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/ribbonstyle/ribbonstyle.html
Although I've seen it in other programs, Chimera does not have an option to smoothly taper the ribbon between coil and helix/strand.
In general we recommend sending questions to the mailing list CC'd here, but only if you are not including private data. In this case I don't think it matters what protein structure is involved, so it is a general question ... to which I don't have an answer but maybe others on the list will. I did not include your session in this public message.
Best, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Jan 24, 2022, at 9:37 AM, Qian Zhang qzhang30@gmail.com wrote:
Dear Dr. Meng, I hope you are doing well. I emailed you guys about 4 years ago and got someone to help me write a script to do this but I can't find that script anymore.
What I wanted to achieve is to 'smooth' out the connections between random coil vs. helixes or vs. sheets. Not like the one shown in this picture that the coil just inserts into the start of the sheet.
I've attached a session file (v.1.15) that can be used as a starting point.
The purpose of this is to 3D-print this into a structure and I am afraid all those non-smooth connections are going to break off.
Please let me know. Qian
See for example the "thickened ribbon" examples in this nice publication:
Da Veiga Beltrame, E., Tyrwhitt-Drake, J., Roy, I., Shalaby, R., Suckale, J., Pomeranz Krummel, D. 3D Printing of Biomolecular Models for Research and Pedagogy. <em>J. Vis. Exp.</em> (121), e55427, doi:10.3791/55427 (2017). https://www.jove.com/t/55427/3d-printing-of-biomolecular-models-for-research-and-pedagogy
They used the Chimera tool "Ribbon Style Editor."
Elaine
On Jan 24, 2022, at 11:03 AM, Elaine Meng via Chimera-users chimera-users@cgl.ucsf.edu wrote:
Hi Qian, I don't know of any way to "smooth" those junctions between coil and helix/strand, but I believe that many people 3D print the ribbons and they have not been a problem as long as you make the overall ribbon thick enough, e.g. with the "struts" command or Ribbon Style Editor.
https://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/struts.html https://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/ribbonstyle/ribbonstyle.html
Although I've seen it in other programs, Chimera does not have an option to smoothly taper the ribbon between coil and helix/strand.
In general we recommend sending questions to the mailing list CC'd here, but only if you are not including private data. In this case I don't think it matters what protein structure is involved, so it is a general question ... to which I don't have an answer but maybe others on the list will. I did not include your session in this public message.
Best, Elaine
Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Jan 24, 2022, at 9:37 AM, Qian Zhang qzhang30@gmail.com wrote:
Dear Dr. Meng, I hope you are doing well. I emailed you guys about 4 years ago and got someone to help me write a script to do this but I can't find that script anymore.
What I wanted to achieve is to 'smooth' out the connections between random coil vs. helixes or vs. sheets. Not like the one shown in this picture that the coil just inserts into the start of the sheet.
<image.png>
I've attached a session file (v.1.15) that can be used as a starting point.
The purpose of this is to 3D-print this into a structure and I am afraid all those non-smooth connections are going to break off.
Please let me know. Qian
Chimera-users mailing list: Chimera-users@cgl.ucsf.edu Manage subscription: https://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users
Hi Dr. Meng, I know Chimera doesn't have this function but a few years ago you referred me to another person (maybe Dr. Huang? I can't remember) who actually wrote a few lines of python code that did exactly what I needed. He emailed me the script and I ran it by Chimera. I left that company so I can't find the email anymore.
I already used Ribbon Style Editor to get to this step, if I can't figure it out then we will live with this version. Any chance Dr. Huang can look at this problem?
Qian
On Mon, Jan 24, 2022 at 2:03 PM Elaine Meng meng@cgl.ucsf.edu wrote:
Hi Qian, I don't know of any way to "smooth" those junctions between coil and helix/strand, but I believe that many people 3D print the ribbons and they have not been a problem as long as you make the overall ribbon thick enough, e.g. with the "struts" command or Ribbon Style Editor.
https://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/struts.html < https://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/ribbonstyle/ribbo...
Although I've seen it in other programs, Chimera does not have an option to smoothly taper the ribbon between coil and helix/strand.
In general we recommend sending questions to the mailing list CC'd here, but only if you are not including private data. In this case I don't think it matters what protein structure is involved, so it is a general question ... to which I don't have an answer but maybe others on the list will. I did not include your session in this public message.
Best, Elaine
Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Jan 24, 2022, at 9:37 AM, Qian Zhang qzhang30@gmail.com wrote:
Dear Dr. Meng, I hope you are doing well. I emailed you guys about 4 years ago and got someone to help me write a script to do this but I can't find that script anymore.
What I wanted to achieve is to 'smooth' out the connections between random coil vs. helixes or vs. sheets. Not like the one shown in this picture that the coil just inserts into the start of the sheet.
I've attached a session file (v.1.15) that can be used as a starting point.
The purpose of this is to 3D-print this into a structure and I am afraid all those non-smooth connections are going to break off.
Please let me know. Qian
Sorry, he retired a couple of years ago!
I looked in the archive for chimera-users@cgl.ucsf.edu and didn't find anything, but maybe you did not communicate over this forum. (Another advantage of using this address is the archive!) https://www.rbvi.ucsf.edu/chimera/docs/feedback.html
Elaine
On Jan 24, 2022, at 11:26 AM, Qian Zhang via Chimera-users chimera-users@cgl.ucsf.edu wrote:
Hi Dr. Meng, I know Chimera doesn't have this function but a few years ago you referred me to another person (maybe Dr. Huang? I can't remember) who actually wrote a few lines of python code that did exactly what I needed. He emailed me the script and I ran it by Chimera. I left that company so I can't find the email anymore.
I already used Ribbon Style Editor to get to this step, if I can't figure it out then we will live with this version. Any chance Dr. Huang can look at this problem?
Qian
On Mon, Jan 24, 2022 at 2:03 PM Elaine Meng meng@cgl.ucsf.edu wrote: Hi Qian, I don't know of any way to "smooth" those junctions between coil and helix/strand, but I believe that many people 3D print the ribbons and they have not been a problem as long as you make the overall ribbon thick enough, e.g. with the "struts" command or Ribbon Style Editor.
https://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/struts.html https://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/ribbonstyle/ribbonstyle.html
Although I've seen it in other programs, Chimera does not have an option to smoothly taper the ribbon between coil and helix/strand.
In general we recommend sending questions to the mailing list CC'd here, but only if you are not including private data. In this case I don't think it matters what protein structure is involved, so it is a general question ... to which I don't have an answer but maybe others on the list will. I did not include your session in this public message.
Best, Elaine
Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Jan 24, 2022, at 9:37 AM, Qian Zhang qzhang30@gmail.com wrote:
Dear Dr. Meng, I hope you are doing well. I emailed you guys about 4 years ago and got someone to help me write a script to do this but I can't find that script anymore.
What I wanted to achieve is to 'smooth' out the connections between random coil vs. helixes or vs. sheets. Not like the one shown in this picture that the coil just inserts into the start of the sheet.
<image.png>
I've attached a session file (v.1.15) that can be used as a starting point.
The purpose of this is to 3D-print this into a structure and I am afraid all those non-smooth connections are going to break off.
Please let me know. Qian
Chimera-users mailing list: Chimera-users@cgl.ucsf.edu Manage subscription: https://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users
By the way, I just noticed that there is a bug in the "struts" command of Chimera that makes the ribbon arrowheads backwards. However, we are no longer developing Chimera, so it is unlikely to be fixed.
So if using Chimera, you should use Ribbon Style Editor to thicken the ribbons as described in that JoVE protocol link I sent earlier today.
If you want to use the "struts" command, use ChimeraX instead of Chimera. The ChimeraX struts command does not have this bug.
Elaine
On Jan 24, 2022, at 11:56 AM, Elaine Meng meng@cgl.ucsf.edu wrote:
Sorry, he retired a couple of years ago!
I looked in the archive for chimera-users@cgl.ucsf.edu and didn't find anything, but maybe you did not communicate over this forum. (Another advantage of using this address is the archive!) https://www.rbvi.ucsf.edu/chimera/docs/feedback.html
Elaine
On Jan 24, 2022, at 11:26 AM, Qian Zhang via Chimera-users chimera-users@cgl.ucsf.edu wrote:
Hi Dr. Meng, I know Chimera doesn't have this function but a few years ago you referred me to another person (maybe Dr. Huang? I can't remember) who actually wrote a few lines of python code that did exactly what I needed. He emailed me the script and I ran it by Chimera. I left that company so I can't find the email anymore.
I already used Ribbon Style Editor to get to this step, if I can't figure it out then we will live with this version. Any chance Dr. Huang can look at this problem?
Qian
On Mon, Jan 24, 2022 at 2:03 PM Elaine Meng meng@cgl.ucsf.edu wrote: Hi Qian, I don't know of any way to "smooth" those junctions between coil and helix/strand, but I believe that many people 3D print the ribbons and they have not been a problem as long as you make the overall ribbon thick enough, e.g. with the "struts" command or Ribbon Style Editor.
https://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/struts.html https://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/ribbonstyle/ribbonstyle.html
Although I've seen it in other programs, Chimera does not have an option to smoothly taper the ribbon between coil and helix/strand.
In general we recommend sending questions to the mailing list CC'd here, but only if you are not including private data. In this case I don't think it matters what protein structure is involved, so it is a general question ... to which I don't have an answer but maybe others on the list will. I did not include your session in this public message.
Best, Elaine
Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Jan 24, 2022, at 9:37 AM, Qian Zhang qzhang30@gmail.com wrote:
Dear Dr. Meng, I hope you are doing well. I emailed you guys about 4 years ago and got someone to help me write a script to do this but I can't find that script anymore.
What I wanted to achieve is to 'smooth' out the connections between random coil vs. helixes or vs. sheets. Not like the one shown in this picture that the coil just inserts into the start of the sheet.
<image.png>
I've attached a session file (v.1.15) that can be used as a starting point.
The purpose of this is to 3D-print this into a structure and I am afraid all those non-smooth connections are going to break off.
Please let me know. Qian
Chimera-users mailing list: Chimera-users@cgl.ucsf.edu Manage subscription: https://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users
I will try out! Thanks.
On Mon, Jan 24, 2022 at 3:22 PM Elaine Meng meng@cgl.ucsf.edu wrote:
By the way, I just noticed that there is a bug in the "struts" command of Chimera that makes the ribbon arrowheads backwards. However, we are no longer developing Chimera, so it is unlikely to be fixed.
So if using Chimera, you should use Ribbon Style Editor to thicken the ribbons as described in that JoVE protocol link I sent earlier today.
If you want to use the "struts" command, use ChimeraX instead of Chimera. The ChimeraX struts command does not have this bug.
Elaine
On Jan 24, 2022, at 11:56 AM, Elaine Meng meng@cgl.ucsf.edu wrote:
Sorry, he retired a couple of years ago!
I looked in the archive for chimera-users@cgl.ucsf.edu and didn't find
anything, but maybe you did not communicate over this forum. (Another advantage of using this address is the archive!)
https://www.rbvi.ucsf.edu/chimera/docs/feedback.html
Elaine
On Jan 24, 2022, at 11:26 AM, Qian Zhang via Chimera-users <
chimera-users@cgl.ucsf.edu> wrote:
Hi Dr. Meng, I know Chimera doesn't have this function but a few years ago you
referred me to another person (maybe Dr. Huang? I can't remember) who actually wrote a few lines of python code that did exactly what I needed. He emailed me the script and I ran it by Chimera. I left that company so I can't find the email anymore.
I already used Ribbon Style Editor to get to this step, if I can't
figure it out then we will live with this version. Any chance Dr. Huang can look at this problem?
Qian
On Mon, Jan 24, 2022 at 2:03 PM Elaine Meng meng@cgl.ucsf.edu wrote: Hi Qian, I don't know of any way to "smooth" those junctions between coil and
helix/strand, but I believe that many people 3D print the ribbons and they have not been a problem as long as you make the overall ribbon thick enough, e.g. with the "struts" command or Ribbon Style Editor.
https://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/struts.html <
https://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/ribbonstyle/ribbo...
Although I've seen it in other programs, Chimera does not have an
option to smoothly taper the ribbon between coil and helix/strand.
In general we recommend sending questions to the mailing list CC'd
here, but only if you are not including private data. In this case I don't think it matters what protein structure is involved, so it is a general question ... to which I don't have an answer but maybe others on the list will. I did not include your session in this public message.
Best, Elaine
Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Jan 24, 2022, at 9:37 AM, Qian Zhang qzhang30@gmail.com wrote:
Dear Dr. Meng, I hope you are doing well. I emailed you guys about 4 years ago and
got someone to help me write a script to do this but I can't find that script anymore.
What I wanted to achieve is to 'smooth' out the connections between
random coil vs. helixes or vs. sheets. Not like the one shown in this picture that the coil just inserts into the start of the sheet.
<image.png>
I've attached a session file (v.1.15) that can be used as a starting
point.
The purpose of this is to 3D-print this into a structure and I am
afraid all those non-smooth connections are going to break off.
Please let me know. Qian
Chimera-users mailing list: Chimera-users@cgl.ucsf.edu Manage subscription:
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Qian Zhang