Dear Blaine, On Fri, Nov 12, 2021 at 10:14 AM Mooers, Blaine H.M. (HSC) < blaine-moo...@ouhsc.edu> 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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