Re: [PyMOL] [EXTERNAL] create a 26 bp RNA from a 13 bp system

[amirhossein t. <tag...@gm...>]

Hi Xiang-Jun,

Sorry to bother. I meant if I can do the same thing you have done with DSSR
pro with free version of x3dna-dssr, as I am getting some error messages:

x3dna-dssr -i=model.pdb --frame-pair=last -o=model1-ref-last.pdb
Processing file 'model.pdb'
total number of nucleotides: 26
[e] no matched residue for option --frame

Thanks for your help.

Best,
Amir


On Fri, Nov 12, 2021 at 11:00 AM Xiang-Jun Lu <3d...@gm...> wrote:

> Hi Amir,
>
> Please have a look at the announcement "No more grant funding for
> 3DNA/DSSR" (
> http://forum.x3dna.org/site-announcements/no-more-grant-funding-for-3dnadssr/)
> on the 3DNA Forum. DSSR results are reproduced, period.
>
> Best wishes,
>
> Xiang-Jun
>
> --
> Xiang-Jun Lu (Ph.D.)
> Email: xia...@x3...
> Web: http://x3dna.org/
> Forum: http://forum.x3dna.org/
>
>
> On Fri, Nov 12, 2021 at 10:51 AM amirhossein taghavi <
> tag...@gm...> wrote:
>
>> Hello Dr. Xiang-Jun Lu,
>>
>> Thanks a lot for your help. The model you have duplicated is exactly what
>> I am looking for (checked it with VMD). Unfortunately I do not have access
>> to DSSR-Pro. Is there any way that I can reproduce your procedure with
>> x3dna-dssr?
>> I need to create different numbers of duplicates (2,4,6,5,8) for
>> different systems and this will be very helpful.
>>
>> Thanks in advance.
>>
>> Best regards,
>> Amir
>>
>> On Fri, Nov 12, 2021 at 10:33 AM Xiang-Jun Lu <3d...@gm...> wrote:
>>
>>> Dear Blaine,
>>>
>>> On Fri, Nov 12, 2021 at 10:14 AM Mooers, Blaine H.M. (HSC) <
>>> Bla...@ou...> wrote:
>>>
>>>> Hi Xiang-Jun Lu,
>>>>
>>>> Thanks for proving me wrong. Congratulations on your duplicated model!
>>>> Please share the commands that you used with DSSR to generate the
>>>> duplicated helix.
>>>>
>>>
>>> The duplicated model was generated with following DSSR Pro commands:
>>>
>>> ```
>>> x3dna-dssr tasks -i=model.pdb --frame-pair=last -o=model1-ref-last.pdb
>>>
>>> x3dna-dssr fiber --seq=GG --rna-ds -o=conn.pdb
>>> x3dna-dssr tasks -i=conn.pdb --frame-pair=first --remove-pair
>>> -o=ref-conn.pdb
>>>
>>> x3dna-dssr tasks --merge-file='model1-ref-last.pdb ref-conn.pdb'
>>> -o=temp1.pdb
>>>
>>> x3dna-dssr tasks -i=temp1.pdb --frame-pair=last --remove-pair
>>> -o=temp2.pdb
>>> x3dna-dssr tasks -i=model.pdb --frame-pair=first -o=model1-ref-first.pdb
>>>
>>> x3dna-dssr tasks --merge-file='temp2.pdb model1-ref-first.pdb'
>>> -o=duplicate-model.pdb
>>> ```
>>>
>>> It takes seconds to run. Moreover, by replacing `--seq=GG` with
>>> `--seq=GA10G` for example, one can easily get a linker with 10 adenines.
>>> The 'GG` is just a space-holder, and can be replaced with any other bases.
>>> The linker sequence could be any bases: eg. A5T3G6, AAATTGG, etc. Users who
>>> want to know more about DSSR can watch the overview video
>>> http://docs.x3dna.org/dssr-overview/ (20m).
>>>
>>>
>>>> PyMOL does not generate the cartoon representation for the backbones of
>>>> your duplicate helix.
>>>> Do you know why?
>>>>
>>>
>>> I noticed the phenomenon but I really do not know why. I used 'as lines'
>>> in PyMOL to verify the duplicated model.
>>>
>>> Best regards,
>>>
>>> Xiang-Jun
>>>
>>> Best regards,
>>>>
>>>> Blaine
>>>>
>>>> Blaine Mooers, Ph.D.
>>>> Associate Professor
>>>> Department of Biochemistry and Molecular Biology, College of Medicine
>>>> Director of the Laboratory of Biomolecular Structure and Function
>>>> Academic Director, Biomolecular Structure Core, COBRE in Structural
>>>> Biology
>>>> Full Member, Cancer Biology Program, Stephenson Cancer Center
>>>> University of Oklahoma Health Sciences Center
>>>>
>>>> Mailing Address:
>>>> 975 NE 10th Street, BRC 466
>>>> Oklahoma City, OK 73104-5419
>>>> Office: 405-271-8300 Lab: 405-271-8312
>>>>
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>>
>>