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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