[chimerax-users] Build DNA structure in Chimera X

[Andreas Göransson]

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 at cgl.ucsf.edu>
Skickat: den 26 november 2020 17:33
Till: Andreas Göransson <andreas.c.goransson at liu.se>
Kopia: ChimeraX Users Help <chimerax-users at 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 at 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 at cgl.ucsf.edu>
> Skickat: den 25 november 2020 20:08
> Till: Andreas Göransson <andreas.c.goransson at liu.se>
> Kopia: chimerax-users <chimerax-users at 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 at 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 at cgl.ucsf.edu>
>> Skickat: den 25 november 2020 17:44
>> Till: Andreas Göransson <andreas.c.goransson at liu.se>
>> Kopia: chimerax-users at cgl.ucsf.edu <chimerax-users at 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 at 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
>>
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