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 <3dna...@gmail.com> 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: 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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