Dear Chimera X users, I have recently switched to Chimera X from the previous version. Do anyone know if there still is a possibility to build DNA structures as in the previous versions of Chimera? THanks in advance, Andreas Best regards Andreas Göransson PhD Student ITN Linköping University Phone +46 11 36 30 79 Visiting address: Hus Kopparhammaren, G518, Campus Norrköping
Hi Andreas, ChimeraX does not yet have DNA building, so for now you would need to use Chimera for that task. We hope to have it in ChimeraX in the future, but I cannot say exactly when. Best, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Nov 25, 2020, at 2:37 AM, Andreas Göransson <andreas.c.goransson@liu.se> wrote:
Dear Chimera X users,
I have recently switched to Chimera X from the previous version. Do anyone know if there still is a possibility to build DNA structures as in the previous versions of Chimera?
THanks in advance, Andreas
Hi Elaine, and thank you for your fast reply! Yes, I suspected that it was not available, just wanted to make sure that I got it right. By the way, do you happen to know why B-DNA built in Chimera has a slight tilt/rotation, i.e. it is not exactly vertical? Sometimes one wants to import the structure into 3D software like Blender to make further processing and animation possible and then it would have been convenient to have it perfectly vertical. Best regards Andreas Göransson PhD Student ITN Linköping University Phone +46 11 36 30 79 Visiting address: Hus Kopparhammaren, G518, Campus Norrköping ________________________________ Från: Elaine Meng <meng@cgl.ucsf.edu> Skickat: den 25 november 2020 17:44 Till: Andreas Göransson <andreas.c.goransson@liu.se> Kopia: chimerax-users@cgl.ucsf.edu <chimerax-users@cgl.ucsf.edu> Ämne: Re: [chimerax-users] Build DNA structure in Chimera X Hi Andreas, ChimeraX does not yet have DNA building, so for now you would need to use Chimera for that task. We hope to have it in ChimeraX in the future, but I cannot say exactly when. Best, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Nov 25, 2020, at 2:37 AM, Andreas Göransson <andreas.c.goransson@liu.se> wrote:
Dear Chimera X users,
I have recently switched to Chimera X from the previous version. Do anyone know if there still is a possibility to build DNA structures as in the previous versions of Chimera?
THanks in advance, Andreas
Hi Andreas, You must be using a very long sequence of base pairs. To my eye, a 100-bp nucleic acid structure built by Chimera looks pretty straight. I would guess that any slight bend/tilt is due to cumulative roundoff error in the transformation matrix as it places one base pair relative to the next. If you need something absolutely straight, two possibilities are: 1) minimize the structure afterward [steepest descent steps only; conjugate gradient will take forever], or 2) use another nucleic-acid builder, such as the "nab" program (nucleic acid builder) from AmberTools (ambermd.org <http://ambermd.org/>). --Eric Eric Pettersen UCSF Computer Graphics Lab
On Nov 25, 2020, at 10:12 AM, Andreas Göransson <andreas.c.goransson@liu.se> wrote:
Hi Elaine, and thank you for your fast reply!
Yes, I suspected that it was not available, just wanted to make sure that I got it right. By the way, do you happen to know why B-DNA built in Chimera has a slight tilt/rotation, i.e. it is not exactly vertical? Sometimes one wants to import the structure into 3D software like Blender to make further processing and animation possible and then it would have been convenient to have it perfectly vertical.
Best regards Andreas Göransson PhD Student ITN Linköping University Phone +46 11 36 30 79 Visiting address: Hus Kopparhammaren, G518, Campus Norrköping
Från: Elaine Meng <meng@cgl.ucsf.edu <mailto:meng@cgl.ucsf.edu>> Skickat: den 25 november 2020 17:44 Till: Andreas Göransson <andreas.c.goransson@liu.se <mailto:andreas.c.goransson@liu.se>> Kopia: chimerax-users@cgl.ucsf.edu <mailto:chimerax-users@cgl.ucsf.edu> <chimerax-users@cgl.ucsf.edu <mailto:chimerax-users@cgl.ucsf.edu>> Ämne: Re: [chimerax-users] Build DNA structure in Chimera X
Hi Andreas, ChimeraX does not yet have DNA building, so for now you would need to use Chimera for that task. We hope to have it in ChimeraX in the future, but I cannot say exactly when. Best, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Nov 25, 2020, at 2:37 AM, Andreas Göransson <andreas.c.goransson@liu.se <mailto:andreas.c.goransson@liu.se>> wrote:
Dear Chimera X users,
I have recently switched to Chimera X from the previous version. Do anyone know if there still is a possibility to build DNA structures as in the previous versions of Chimera?
THanks in advance, Andreas
_______________________________________________ ChimeraX-users mailing list ChimeraX-users@cgl.ucsf.edu <mailto:ChimeraX-users@cgl.ucsf.edu> Manage subscription: https://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users <https://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users>
Hi Eric, Actually, even short sequences do get a tilt - please see attached images from Chimera and the imported model in Blender (same tilt). Best regards Andreas Göransson PhD Student ITN Linköping University Phone +46 11 36 30 79 Visiting address: Hus Kopparhammaren, G518, Campus Norrköping ________________________________ Från: Eric Pettersen <pett@cgl.ucsf.edu> Skickat: den 25 november 2020 20:08 Till: Andreas Göransson <andreas.c.goransson@liu.se> Kopia: chimerax-users <chimerax-users@cgl.ucsf.edu> Ämne: Re: [chimerax-users] Build DNA structure in Chimera X Hi Andreas, You must be using a very long sequence of base pairs. To my eye, a 100-bp nucleic acid structure built by Chimera looks pretty straight. I would guess that any slight bend/tilt is due to cumulative roundoff error in the transformation matrix as it places one base pair relative to the next. If you need something absolutely straight, two possibilities are: 1) minimize the structure afterward [steepest descent steps only; conjugate gradient will take forever], or 2) use another nucleic-acid builder, such as the "nab" program (nucleic acid builder) from AmberTools (ambermd.org<http://ambermd.org>). --Eric Eric Pettersen UCSF Computer Graphics Lab On Nov 25, 2020, at 10:12 AM, Andreas Göransson <andreas.c.goransson@liu.se<mailto:andreas.c.goransson@liu.se>> wrote: Hi Elaine, and thank you for your fast reply! Yes, I suspected that it was not available, just wanted to make sure that I got it right. By the way, do you happen to know why B-DNA built in Chimera has a slight tilt/rotation, i.e. it is not exactly vertical? Sometimes one wants to import the structure into 3D software like Blender to make further processing and animation possible and then it would have been convenient to have it perfectly vertical. Best regards Andreas Göransson PhD Student ITN Linköping University Phone +46 11 36 30 79 Visiting address: Hus Kopparhammaren, G518, Campus Norrköping ________________________________ Från: Elaine Meng <meng@cgl.ucsf.edu<mailto:meng@cgl.ucsf.edu>> Skickat: den 25 november 2020 17:44 Till: Andreas Göransson <andreas.c.goransson@liu.se<mailto:andreas.c.goransson@liu.se>> Kopia: chimerax-users@cgl.ucsf.edu<mailto:chimerax-users@cgl.ucsf.edu> <chimerax-users@cgl.ucsf.edu<mailto:chimerax-users@cgl.ucsf.edu>> Ämne: Re: [chimerax-users] Build DNA structure in Chimera X Hi Andreas, ChimeraX does not yet have DNA building, so for now you would need to use Chimera for that task. We hope to have it in ChimeraX in the future, but I cannot say exactly when. Best, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Nov 25, 2020, at 2:37 AM, Andreas Göransson <andreas.c.goransson@liu.se<mailto:andreas.c.goransson@liu.se>> wrote:
Dear Chimera X users,
I have recently switched to Chimera X from the previous version. Do anyone know if there still is a possibility to build DNA structures as in the previous versions of Chimera?
THanks in advance, Andreas
_______________________________________________ ChimeraX-users mailing list ChimeraX-users@cgl.ucsf.edu<mailto:ChimeraX-users@cgl.ucsf.edu> Manage subscription: https://plato.cgl.ucsf.edu/mailman/listinfo/chimerax-users
Hi Andreas, Eric may have thought you meant it was crooked (internal coordinates) rather than straight but tilted. In any case, Chimera doesn't build nucleic acids by placement around an axis, but by joining successive templates using specific bond lengths and angles. If you need it to be exactly vertical, you could rotate it yourself and then save transformed coordinates from Chimera. Alternatively, you could use some other program for building nucleic acids, but I don't know if other programs would make the result exactly vertical either. Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Nov 25, 2020, at 11:29 PM, Andreas Göransson <andreas.c.goransson@liu.se> wrote:
Hi Eric,
Actually, even short sequences do get a tilt - please see attached images from Chimera and the imported model in Blender (same tilt).
Best regards Andreas Göransson PhD Student ITN Linköping University Phone +46 11 36 30 79 Visiting address: Hus Kopparhammaren, G518, Campus Norrköping
Från: Eric Pettersen <pett@cgl.ucsf.edu> Skickat: den 25 november 2020 20:08 Till: Andreas Göransson <andreas.c.goransson@liu.se> Kopia: chimerax-users <chimerax-users@cgl.ucsf.edu> Ämne: Re: [chimerax-users] Build DNA structure in Chimera X
Hi Andreas, You must be using a very long sequence of base pairs. To my eye, a 100-bp nucleic acid structure built by Chimera looks pretty straight. I would guess that any slight bend/tilt is due to cumulative roundoff error in the transformation matrix as it places one base pair relative to the next. If you need something absolutely straight, two possibilities are: 1) minimize the structure afterward [steepest descent steps only; conjugate gradient will take forever], or 2) use another nucleic-acid builder, such as the "nab" program (nucleic acid builder) from AmberTools (ambermd.org).
--Eric
Eric Pettersen UCSF Computer Graphics Lab
On Nov 25, 2020, at 10:12 AM, Andreas Göransson <andreas.c.goransson@liu.se> wrote:
Hi Elaine, and thank you for your fast reply!
Yes, I suspected that it was not available, just wanted to make sure that I got it right. By the way, do you happen to know why B-DNA built in Chimera has a slight tilt/rotation, i.e. it is not exactly vertical? Sometimes one wants to import the structure into 3D software like Blender to make further processing and animation possible and then it would have been convenient to have it perfectly vertical.
Best regards Andreas Göransson PhD Student ITN Linköping University Phone +46 11 36 30 79 Visiting address: Hus Kopparhammaren, G518, Campus Norrköping
Från: Elaine Meng <meng@cgl.ucsf.edu> Skickat: den 25 november 2020 17:44 Till: Andreas Göransson <andreas.c.goransson@liu.se> Kopia: chimerax-users@cgl.ucsf.edu <chimerax-users@cgl.ucsf.edu> Ämne: Re: [chimerax-users] Build DNA structure in Chimera X
Hi Andreas, ChimeraX does not yet have DNA building, so for now you would need to use Chimera for that task. We hope to have it in ChimeraX in the future, but I cannot say exactly when. Best, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Nov 25, 2020, at 2:37 AM, Andreas Göransson <andreas.c.goransson@liu.se> wrote:
Dear Chimera X users,
I have recently switched to Chimera X from the previous version. Do anyone know if there still is a possibility to build DNA structures as in the previous versions of Chimera?
THanks in advance, Andreas
_______________________________________________ ChimeraX-users mailing list ChimeraX-users@cgl.ucsf.edu Manage subscription: https://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users
<Skärmavbild 2020-11-26 kl. 08.24.25.png><Skärmavbild 2020-11-26 kl. 08.25.37.png>_______________________________________________ ChimeraX-users mailing list ChimeraX-users@cgl.ucsf.edu Manage subscription: https://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users
Hi Elaine, Yes I realized that afterwards. Thanks for all help, I have found out other alternatives. We need very symmetrical models since we are building an interactive web application where students will build their own DNA against a template strand, that's why we need a symmetrical molecule. Best /Andreas Best regards Andreas Göransson PhD Student ITN Linköping University Phone +46 11 36 30 79 Visiting address: Hus Kopparhammaren, G518, Campus Norrköping ________________________________ Från: Elaine Meng <meng@cgl.ucsf.edu> Skickat: den 26 november 2020 17:33 Till: Andreas Göransson <andreas.c.goransson@liu.se> Kopia: ChimeraX Users Help <chimerax-users@cgl.ucsf.edu> Ämne: Re: [chimerax-users] Build DNA structure in Chimera X Hi Andreas, Eric may have thought you meant it was crooked (internal coordinates) rather than straight but tilted. In any case, Chimera doesn't build nucleic acids by placement around an axis, but by joining successive templates using specific bond lengths and angles. If you need it to be exactly vertical, you could rotate it yourself and then save transformed coordinates from Chimera. Alternatively, you could use some other program for building nucleic acids, but I don't know if other programs would make the result exactly vertical either. Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Nov 25, 2020, at 11:29 PM, Andreas Göransson <andreas.c.goransson@liu.se> wrote:
Hi Eric,
Actually, even short sequences do get a tilt - please see attached images from Chimera and the imported model in Blender (same tilt).
Best regards Andreas Göransson PhD Student ITN Linköping University Phone +46 11 36 30 79 Visiting address: Hus Kopparhammaren, G518, Campus Norrköping
Från: Eric Pettersen <pett@cgl.ucsf.edu> Skickat: den 25 november 2020 20:08 Till: Andreas Göransson <andreas.c.goransson@liu.se> Kopia: chimerax-users <chimerax-users@cgl.ucsf.edu> Ämne: Re: [chimerax-users] Build DNA structure in Chimera X
Hi Andreas, You must be using a very long sequence of base pairs. To my eye, a 100-bp nucleic acid structure built by Chimera looks pretty straight. I would guess that any slight bend/tilt is due to cumulative roundoff error in the transformation matrix as it places one base pair relative to the next. If you need something absolutely straight, two possibilities are: 1) minimize the structure afterward [steepest descent steps only; conjugate gradient will take forever], or 2) use another nucleic-acid builder, such as the "nab" program (nucleic acid builder) from AmberTools (ambermd.org).
--Eric
Eric Pettersen UCSF Computer Graphics Lab
On Nov 25, 2020, at 10:12 AM, Andreas Göransson <andreas.c.goransson@liu.se> wrote:
Hi Elaine, and thank you for your fast reply!
Yes, I suspected that it was not available, just wanted to make sure that I got it right. By the way, do you happen to know why B-DNA built in Chimera has a slight tilt/rotation, i.e. it is not exactly vertical? Sometimes one wants to import the structure into 3D software like Blender to make further processing and animation possible and then it would have been convenient to have it perfectly vertical.
Best regards Andreas Göransson PhD Student ITN Linköping University Phone +46 11 36 30 79 Visiting address: Hus Kopparhammaren, G518, Campus Norrköping
Från: Elaine Meng <meng@cgl.ucsf.edu> Skickat: den 25 november 2020 17:44 Till: Andreas Göransson <andreas.c.goransson@liu.se> Kopia: chimerax-users@cgl.ucsf.edu <chimerax-users@cgl.ucsf.edu> Ämne: Re: [chimerax-users] Build DNA structure in Chimera X
Hi Andreas, ChimeraX does not yet have DNA building, so for now you would need to use Chimera for that task. We hope to have it in ChimeraX in the future, but I cannot say exactly when. Best, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Nov 25, 2020, at 2:37 AM, Andreas Göransson <andreas.c.goransson@liu.se> wrote:
Dear Chimera X users,
I have recently switched to Chimera X from the previous version. Do anyone know if there still is a possibility to build DNA structures as in the previous versions of Chimera?
THanks in advance, Andreas
_______________________________________________ ChimeraX-users mailing list ChimeraX-users@cgl.ucsf.edu Manage subscription: https://plato.cgl.ucsf.edu/mailman/listinfo/chimerax-users
<Skärmavbild 2020-11-26 kl. 08.24.25.png><Skärmavbild 2020-11-26 kl. 08.25.37.png>_______________________________________________ ChimeraX-users mailing list ChimeraX-users@cgl.ucsf.edu Manage subscription: https://plato.cgl.ucsf.edu/mailman/listinfo/chimerax-users
participants (3)
-
Andreas Göransson -
Elaine Meng -
Eric Pettersen