Dear Chimera Team, first of all, I would like to thank you for providing a sotfware solution to molecular visualization and by the way 3D- printing. I send you this message concerning the UCSF Chimera X version. We usually are preparing our 3D-printing files from data collected from the pdb and to ensure the rigidity of the system, we thick the ribbon size and also add some H-bonds (mainly for helices). However, we are not able to find the way to do it in this version. In the previous version (1.17), the command line was : Tools-depiction-ribbon style editor Could you explain us the new procedure to make this ? We also noticed that the opportunity to save the file in a stl extension was not allowed in the 1.17 version. This option is running in the X version. Thank you very much for your reply Best regards. fhporee François-Hugues Porée Professeur de Chimie Thérapeutique Institut des Sciences Chimiques de Rennes UMR CNRS 6226 Faculté de Pharmacie - Université de Rennes 2 Avenue du Pr Léon Bernard F-35043 Rennes France Tel.02 23 23 41 87
Dear François-Hugues Porée, In ChimeraX, there is no GUI tool but you can use the "cartoon style" command to increase ribbon (cartoon) width and thickness to specific angstrom values. For details see the help: <https://rbvi.ucsf.edu/chimerax/docs/user/commands/cartoon.html#style> However, ChimeraX also has a "struts" command that will automatically increase ribbon thickness in addition to adding some stick pseudobonds specifically to make a 3D model stronger. So you may want to use "struts" instead : <https://rbvi.ucsf.edu/chimerax/docs/user/commands/struts.html> Another thing to consider for 3D printing is the number of triangles of the object, which you can adjust with "graphics quality": <https://rbvi.ucsf.edu/chimerax/docs/user/commands/graphics.html#quality> For ChimeraX questions in the future, you may want to use the other address chimerax-users@cgl.ucsf.edu (CC'd here) -- since the answers are different for the two programs, we try to not confuse people between them. I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco P.S. you may also be interested in the NIH 3D website: <https://3d.nih.gov/>
On May 15, 2023, at 6:58 AM, Francois-Hugues Poree via Chimera-users <chimera-users@cgl.ucsf.edu> wrote:
Dear Chimera Team, first of all, I would like to thank you for providing a sotfware solution to molecular visualization and by the way 3D-printing.
I send you this message concerning the UCSF Chimera X version. We usually are preparing our 3D-printing files from data collected from the pdb and to ensure the rigidity of the system, we thick the ribbon size and also add some H-bonds (mainly for helices). However, we are not able to find the way to do it in this version. In the previous version (1.17), the command line was : Tools-depiction-ribbon style editor
Could you explain us the new procedure to make this ?
We also noticed that the opportunity to save the file in a stl extension was not allowed in the 1.17 version. This option is running in the X version.
Thank you very much for your reply
Best regards.
fhporee
François-Hugues Porée Professeur de Chimie Thérapeutique Institut des Sciences Chimiques de Rennes UMR CNRS 6226 Faculté de Pharmacie - Université de Rennes 2 Avenue du Pr Léon Bernard F-35043 Rennes France Tel.02 23 23 41 87
Also, the NIHPresets <https://cxtoolshed.rbvi.ucsf.edu/apps/chimeraxnihpresets> bundle on the toolshed has several presets useful for 3D printing. --Eric Eric Pettersen UCSF Computer Graphics Lab
On May 15, 2023, at 9:57 AM, Elaine Meng via Chimera-users <chimera-users@cgl.ucsf.edu> wrote:
Dear François-Hugues Porée, In ChimeraX, there is no GUI tool but you can use the "cartoon style" command to increase ribbon (cartoon) width and thickness to specific angstrom values. For details see the help: <https://rbvi.ucsf.edu/chimerax/docs/user/commands/cartoon.html#style>
However, ChimeraX also has a "struts" command that will automatically increase ribbon thickness in addition to adding some stick pseudobonds specifically to make a 3D model stronger. So you may want to use "struts" instead : <https://rbvi.ucsf.edu/chimerax/docs/user/commands/struts.html>
Another thing to consider for 3D printing is the number of triangles of the object, which you can adjust with "graphics quality": <https://rbvi.ucsf.edu/chimerax/docs/user/commands/graphics.html#quality>
For ChimeraX questions in the future, you may want to use the other address chimerax-users@cgl.ucsf.edu (CC'd here) -- since the answers are different for the two programs, we try to not confuse people between them.
I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
P.S. you may also be interested in the NIH 3D website: <https://3d.nih.gov/>
On May 15, 2023, at 6:58 AM, Francois-Hugues Poree via Chimera-users <chimera-users@cgl.ucsf.edu> wrote:
Dear Chimera Team, first of all, I would like to thank you for providing a sotfware solution to molecular visualization and by the way 3D-printing.
I send you this message concerning the UCSF Chimera X version. We usually are preparing our 3D-printing files from data collected from the pdb and to ensure the rigidity of the system, we thick the ribbon size and also add some H-bonds (mainly for helices). However, we are not able to find the way to do it in this version. In the previous version (1.17), the command line was : Tools-depiction-ribbon style editor
Could you explain us the new procedure to make this ?
We also noticed that the opportunity to save the file in a stl extension was not allowed in the 1.17 version. This option is running in the X version.
Thank you very much for your reply
Best regards.
fhporee
François-Hugues Porée Professeur de Chimie Thérapeutique Institut des Sciences Chimiques de Rennes UMR CNRS 6226 Faculté de Pharmacie - Université de Rennes 2 Avenue du Pr Léon Bernard F-35043 Rennes France Tel.02 23 23 41 87
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On behalf of “NIHPresets”, I also invite everyone to check out https://3d.nih.gov<https://3d.nih.gov/> as an easy way to produce 3D print-ready models from molecular structure files (PDB, etc.) From: Chimera-users <chimera-users-bounces@cgl.ucsf.edu> on behalf of Eric Pettersen via Chimera-users <chimera-users@cgl.ucsf.edu> Date: Monday, May 15, 2023 at 1:18 PM To: Oliver Clarke via ChimeraX-users <chimerax-users@cgl.ucsf.edu>, Elaine Meng <meng@cgl.ucsf.edu> Cc: Aissata Gassama <aissata.gassama@univ-rennes.fr>, Francois-Hugues Poree <francois-hugues.poree@univ-rennes.fr>, chimera-users@cgl.ucsf.edu List <chimera-users@cgl.ucsf.edu> Subject: [EXTERNAL] Re: [Chimera-users] 3D_printing Also, the NIHPresets<https://cxtoolshed.rbvi.ucsf.edu/apps/chimeraxnihpresets> bundle on the toolshed has several presets useful for 3D printing. --Eric Eric Pettersen UCSF Computer Graphics Lab On May 15, 2023, at 9:57 AM, Elaine Meng via Chimera-users <chimera-users@cgl.ucsf.edu> wrote: Dear François-Hugues Porée, In ChimeraX, there is no GUI tool but you can use the "cartoon style" command to increase ribbon (cartoon) width and thickness to specific angstrom values. For details see the help: <https://rbvi.ucsf.edu/chimerax/docs/user/commands/cartoon.html#style> However, ChimeraX also has a "struts" command that will automatically increase ribbon thickness in addition to adding some stick pseudobonds specifically to make a 3D model stronger. So you may want to use "struts" instead : <https://rbvi.ucsf.edu/chimerax/docs/user/commands/struts.html> Another thing to consider for 3D printing is the number of triangles of the object, which you can adjust with "graphics quality": <https://rbvi.ucsf.edu/chimerax/docs/user/commands/graphics.html#quality> For ChimeraX questions in the future, you may want to use the other address chimerax-users@cgl.ucsf.edu (CC'd here) -- since the answers are different for the two programs, we try to not confuse people between them. I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco P.S. you may also be interested in the NIH 3D website: <https://3d.nih.gov/> On May 15, 2023, at 6:58 AM, Francois-Hugues Poree via Chimera-users <chimera-users@cgl.ucsf.edu> wrote: Dear Chimera Team, first of all, I would like to thank you for providing a sotfware solution to molecular visualization and by the way 3D-printing. I send you this message concerning the UCSF Chimera X version. We usually are preparing our 3D-printing files from data collected from the pdb and to ensure the rigidity of the system, we thick the ribbon size and also add some H-bonds (mainly for helices). However, we are not able to find the way to do it in this version. In the previous version (1.17), the command line was : Tools-depiction-ribbon style editor Could you explain us the new procedure to make this ? We also noticed that the opportunity to save the file in a stl extension was not allowed in the 1.17 version. This option is running in the X version. Thank you very much for your reply Best regards. fhporee François-Hugues Porée Professeur de Chimie Thérapeutique Institut des Sciences Chimiques de Rennes UMR CNRS 6226 Faculté de Pharmacie - Université de Rennes 2 Avenue du Pr Léon Bernard F-35043 Rennes France Tel.02 23 23 41 87 _______________________________________________ Chimera-users mailing list: Chimera-users@cgl.ucsf.edu Manage subscription: https://www.rbvi.ucsf.edu/mailman/listinfo/chimera-users CAUTION: This email originated from outside of the organization. Do not click links or open attachments unless you recognize the sender and are confident the content is safe.
Dear Dr Meng and Pettersen, thank you very much for your kind and helpful reply. Of course, it helps as we are beginner in this game. All the suggestions are welcomed. Best regards. fhporee François-Hugues Porée Professeur de Chimie Thérapeutique Institut des Sciences Chimiques de Rennes UMR CNRS 6226 Faculté de Pharmacie - Université de Rennes 2 Avenue du Pr Léon Bernard F-35043 Rennes France Tel.02 23 23 41 87 ----- Mail original ----- De: "Elaine Meng" <meng@cgl.ucsf.edu> À: "francois-hugues poree" <francois-hugues.poree@univ-rennes.fr> Cc: "chimera-users@cgl.ucsf.edu List" <chimera-users@cgl.ucsf.edu>, "Aissata Gassama" <aissata.gassama@univ-rennes.fr>, "Oliver Clarke via ChimeraX-users" <chimerax-users@cgl.ucsf.edu> Envoyé: Lundi 15 Mai 2023 18:57:17 Objet: Re: [Chimera-users] 3D_printing Dear François-Hugues Porée, In ChimeraX, there is no GUI tool but you can use the "cartoon style" command to increase ribbon (cartoon) width and thickness to specific angstrom values. For details see the help: <https://rbvi.ucsf.edu/chimerax/docs/user/commands/cartoon.html#style> However, ChimeraX also has a "struts" command that will automatically increase ribbon thickness in addition to adding some stick pseudobonds specifically to make a 3D model stronger. So you may want to use "struts" instead : <https://rbvi.ucsf.edu/chimerax/docs/user/commands/struts.html> Another thing to consider for 3D printing is the number of triangles of the object, which you can adjust with "graphics quality": <https://rbvi.ucsf.edu/chimerax/docs/user/commands/graphics.html#quality> For ChimeraX questions in the future, you may want to use the other address chimerax-users@cgl.ucsf.edu (CC'd here) -- since the answers are different for the two programs, we try to not confuse people between them. I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco P.S. you may also be interested in the NIH 3D website: <https://3d.nih.gov/>
On May 15, 2023, at 6:58 AM, Francois-Hugues Poree via Chimera-users <chimera-users@cgl.ucsf.edu> wrote:
Dear Chimera Team, first of all, I would like to thank you for providing a sotfware solution to molecular visualization and by the way 3D-printing.
I send you this message concerning the UCSF Chimera X version. We usually are preparing our 3D-printing files from data collected from the pdb and to ensure the rigidity of the system, we thick the ribbon size and also add some H-bonds (mainly for helices). However, we are not able to find the way to do it in this version. In the previous version (1.17), the command line was : Tools-depiction-ribbon style editor
Could you explain us the new procedure to make this ?
We also noticed that the opportunity to save the file in a stl extension was not allowed in the 1.17 version. This option is running in the X version.
Thank you very much for your reply
Best regards.
fhporee
François-Hugues Porée Professeur de Chimie Thérapeutique Institut des Sciences Chimiques de Rennes UMR CNRS 6226 Faculté de Pharmacie - Université de Rennes 2 Avenue du Pr Léon Bernard F-35043 Rennes France Tel.02 23 23 41 87
participants (4)
-
Elaine Meng -
Eric Pettersen -
Francois-Hugues Poree -
Hurt, Darrell (NIH/NIAID) [E]