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: xiang...@x3dna.org Web: http://x3dna.org/ Forum: http://forum.x3dna.org/ On Fri, Nov 12, 2021 at 10:51 AM amirhossein taghavi < taghavi.amirhoss...@gmail.com> 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 <3dna...@gmail.com> wrote: > >> 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 >>> >> _______________________________________________ >> PyMOL-users mailing list >> Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net >> Unsubscribe: >> https://sourceforge.net/projects/pymol/lists/pymol-users/unsubscribe > >
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