[PyMOL] Reproduce results in the DSSR paper
A paper titled "DSSR, an integrated software tool for dissecting the spatial structure of RNA" recently appeared in *Nucleic Acids Research* ( http://nar.oxfordjournals.org/cgi/content/full/gkv716). Starting from a three-dimensional atomic coordinate file in either PDB or PDBx/mmCIF format, DSSR, the new software product described in the paper, analyzes and annotates RNA tertiary structures and uncovers a broad range of structural features in a consistent and easily accessible framework. The software is implemented in ANSI C as a stand-alone, command-line program and is self-contained. The binaries for common operating systems (Mac OS X, Linux, and Windows) are tiny (<1MB), without runtime dependencies on third-party libraries. DSSR is efficient and robust due to comprehensive tests against all nucleic-acid-containing structures in the PDB and continued refinements based on user feedback. DSSR identifies canonical and noncanonical base pairs, including those with modified nucleotides, in any tautomeric or protonation state. The software detects higher-order (three or more) coplanar base associations, termed multiplets. It finds arrays of stacked pairs, classifies them by base-pair identity and backbone connectivity, and distinguishes a stem of covalently connected canonical pairs from a helix of stacked pairs of arbitrary type/linkage. DSSR also pinpoints the coaxial stacking of multiple stems within a single helix and lists the isolated canonical pairs that lie outside of a stem. The program characterizes "closed" loops of various types (hairpin, bulge, internal, and junction loops) and pseudoknots of high complexity. Notably, DSSR employs isolated pairs and the ends of stems, whether pseudoknotted or not, to define junction loops. This new, inclusive definition provides a novel perspective on the spatial organization of RNA, even for small molecules such as the viral tRNA mimic from turnip yellow mosaic virus and the *env22* twister ribozyme. In short, DSSR is to RNA what DSSP is to proteins for defining secondary structures, but with more functionality: DSSR includes quantitative descriptions of local base-pair geometry; assignments of common names and classifications of base pairs; listings of commonly used sugar-phosphate backbone parameters, continuous base stacks, and non-pairing interactions (including those involving phosphate groups); and detections of ribose zipper motifs, A-minor motifs, G-tetrads, U-turns, kissing loops, and kink-turns. The publication includes significant new scientific findings that are enabled by the innovative analysis algorithms implemented in the software. Moreover, the paper introduces an appealing and highly informative "cartoon-block" representation of RNA structure that combines PyMOL cartoon schematics with color-coded rectangular base (or base-pair) blocks. As a follow-up to the publication, the 3DNA Forum includes all of the scripts and data files associated with the article in a new section titled "DSSR-NAR paper" (http://forum.x3dna.org/dssr-nar-paper/). The Forum also contains links to an updated version of the DSSR User Manual ( http://x3dna.bio.columbia.edu/docs/dssr-manual.pdf). Any interested party should be able to reproduce the tabulated data and figures (including the supplementary data) reported in the article. Moreover, with the details provided in "RNA cartoon-block representations with PyMOL and DSSR" ( http://forum.x3dna.org/dssr-nar-paper/rna-cartoon-block-representations-with-pymol-and-dssr/), schematic images identical to those in the paper and the post can be easily generated. Any questions related to the paper are welcomed on the 3DNA Forum. Dr. Xiang-Jun Lu, the lead author of the paper and the person spearheading the Forum, aims to respond promptly to any reported issues. [This message is cross-posted on ccp4bb, pdb-l, and pymol-users. I apologize for any duplicate copies you may receive.] Xiang-Jun -- Xiang-Jun Lu (PhD) Email: xiang...@x3dna.org Web: http://x3dna.org/ Forum: http://forum.x3dna.org/ -- ___ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
[PyMOL] issue with label command as in: label *, name; color red
I am surprised by the PyMOL error message with the following commands: # this is fine color red; label *, name # reversing the order causes problems label *, name; color red = PyMOL>label *, name; color red File "", line 1 name; color red ^ SyntaxError: invalid syntax Label-Error: failed to compile expression Label: labelled 0 atoms. = Replacing 'name' with 'resi' or 'resn' etc has the same result. Issuing each command separately works as expected. The error message shows up only if "label *, name" is followed by another command, on the same line. I am using "Version 1.8.7.0 Open-Source" on macOS. Any ideas? Thanks, Xiang-Jun -- Xiang-Jun Lu (Ph.D.) Email: xiang...@x3dna.org Web: http://x3dna.org/ Forum: http://forum.x3dna.org/ ___ 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
[PyMOL] DSSR-enabled innovative schematics of 3D nucleic acid structures with PyMOL
I am glad to announce that the paper, titled "DSSR-enabled innovative schematics of 3D nucleic acid structures with PyMOL", has recently been published in _Nucleic Acids Research_ (https://doi.org/10.1093/nar/gkz1222). The DSSR program creates schematic block representations in diverse styles that can be seamlessly integrated into PyMOL and complement its other popular visualization options. In addition to portraying individual base blocks, DSSR can draw Watson-Crick pairs as long blocks and highlight the minor-groove edges. Notably, DSSR can dramatically simplify the depiction of G-quadruplexes by automatically detecting G-tetrads and treating them as large square blocks. The DSSR-enabled innovative schematics with PyMOL are aesthetically pleasing and highly informative: the base identity, pairing geometry, stacking interactions, double-helical stems, and G-quadruplexes are immediately obvious. These features can be accessed via four interfaces: the command-line interface, the DSSR plugin for PyMOL (written by Thomas Holder; http://pymolwiki.org/index.php/dssr_block), the web application (http://skmatic.x3dna.org/), and the web application programming interface. The web application interface (http://skmatic.x3dna.org/) also provides pre-calculated schematics and meta information of nucleic-acid-containing structures in the PDB. Here are some examples: * http://skmatic.x3dna.org/pdb/2lx1 * http://skmatic.x3dna.org/pdb/2grb * http://skmatic.x3dna.org/pdb/6vu1 * http://skmatic.x3dna.org/pdb_entries # 12 random entries * http://skmatic.x3dna.org/pdb_entries/recent-week * http://skmatic.x3dna.org/pdb_entries/recent-month The supplemental PDF (http://skmatic.x3dna.org/gkaa426-supp.pdf) has been written to serve as a practical guide, with complete and reproducible examples. Best regards, Xiang-Jun -- Xiang-Jun Lu (Ph.D.) Email: xiang...@x3dna.org Web: http://x3dna.org/ Forum: http://forum.x3dna.org/ ___ 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
Re: [PyMOL] DSSR-enabled innovative schematics of 3D nucleic acid structures with PyMOL
> > I thought that some of the list members may be interested in the paper, > titled "DSSR-enabled innovative schematics of 3D nucleic acid structures > with PyMOL", recently published in _Nucleic Acids Research_ ( > https://doi.org/10.1093/nar/gkz1222). *Sorry* about the wrong link to nar/gkz1222 -- I was reading that interesting paper on the U•A-U-rich RNA triple helix. The correct URL to the DSSR-PyMOL NAR paper is: https://doi.org/10.1093/nar/gkaa426 Best regards, Xiang-Jun -- Xiang-Jun Lu (Ph.D.) Email: xiang...@x3dna.org Web: http://x3dna.org/ Forum: http://forum.x3dna.org/ On Sat, May 23, 2020 at 1:41 PM Xiang-Jun Lu <3dna...@gmail.com> wrote: > I am glad to announce that the paper, titled "DSSR-enabled innovative > schematics of 3D nucleic acid structures with PyMOL", has recently been > published in _Nucleic Acids Research_ (https://doi.org/10.1093/nar/gkz1222). > > > The DSSR program creates schematic block representations in diverse styles > that can be seamlessly integrated into PyMOL and complement its other > popular visualization options. In addition to portraying individual base > blocks, DSSR can draw Watson-Crick pairs as long blocks and highlight the > minor-groove edges. Notably, DSSR can dramatically simplify the depiction > of G-quadruplexes by automatically detecting G-tetrads and treating them as > large square blocks. The DSSR-enabled innovative schematics with PyMOL are > aesthetically pleasing and highly informative: the base identity, pairing > geometry, stacking interactions, double-helical stems, and G-quadruplexes > are immediately obvious. These features can be accessed via four > interfaces: the command-line interface, the DSSR plugin for PyMOL (written > by Thomas Holder; http://pymolwiki.org/index.php/dssr_block), the web > application (http://skmatic.x3dna.org/), and the web application > programming interface. > > The web application interface (http://skmatic.x3dna.org/) also provides > pre-calculated schematics and meta information of nucleic-acid-containing > structures in the PDB. Here are some examples: > > * http://skmatic.x3dna.org/pdb/2lx1 > * http://skmatic.x3dna.org/pdb/2grb > * http://skmatic.x3dna.org/pdb/6vu1 > * http://skmatic.x3dna.org/pdb_entries # 12 random entries > * http://skmatic.x3dna.org/pdb_entries/recent-week > * http://skmatic.x3dna.org/pdb_entries/recent-month > > The supplemental PDF (http://skmatic.x3dna.org/gkaa426-supp.pdf) has been > written to serve as a practical guide, with complete and reproducible > examples. > > Best regards, > > Xiang-Jun > > -- > Xiang-Jun Lu (Ph.D.) > Email: xiang...@x3dna.org > Web: http://x3dna.org/ > Forum: http://forum.x3dna.org/ > ___ 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
Re: [PyMOL] [EXTERNAL] create a 26 bp RNA from a 13 bp system
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
Re: [PyMOL] [EXTERNAL] create a 26 bp RNA from a 13 bp system
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 > > ___ 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
Re: [PyMOL] [EXTERNAL] create a 26 bp RNA from a 13 bp system
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 >>> >>> ___ 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
[PyMOL] Cover images of the RNA Journal generated by the NDB using DSSR and PyMOL
Dear list members, I thought it is worth noting that the 2x12 cover images of the *RNA Journal* in 2021 and 2022 have all been generated by the Nucleic Acid Database ( ndbserver.rutgers.edu) using DSSR and PyMOL. See the composite at http://docs.x3dna.org/images/RNAcovers-NDB-dssr-pymol.png and the December 2022 issue at https://rnajournal.cshlp.org/content/28/12.cover-expansion Users can easily generate such highly simplified, yet informative images of nucleic acid structures using http://skmatic.x3dna.org Best regards, Xiang-Jun -- Xiang-Jun Lu (Ph.D.) Email: xiang...@x3dna.org Web: http://x3dna.org/ Forum: http://forum.x3dna.org/ ___ 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
