On Fri, Nov 12, 2021 at 11:15 AM amirhossein taghavi < taghavi.amirhoss...@gmail.com> wrote:
> 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: > No, as made clear in my previous response to Blaine: "The duplicated model was generated with following DSSR Pro commands:" Best regards, Xiang-Jun > 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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