3DNA Forum

Questions and answers => RNA structures (DSSR) => Topic started by: cllawson on July 28, 2020, 02:55:31 pm

Title: RNA Journal Covers
Post by: cllawson on July 28, 2020, 02:55:31 pm: Ha just found this http://docs.x3dna.org/images/3dna-RNA-covers.png
Thank you Xiang-Jun for collating all of the 2019 journal covers I had created using X3DNA/blocview with pymol.
I have been testing out x3dna-dssr --cartoon-block today and it is much easier!
I will be using this great new option for all future NDB requests for covers. :)
Title: Re: RNA Journal Covers
Post by: xiangjun on July 28, 2020, 03:37:38 pm: Hi Cathy,

Thanks for producing all these RNA Journal cover images using 3DNA/blocview and PyMOL; they look nice. In addition to the post on 2019 covers, I also have an update post for 2020, see http://x3dna.org/highlights/cover-images-of-the-rna-journal-in-2020 and the image below. This post is already a bit dated since it does not include the cover of the August 2020 issue.

(http://skmatic.x3dna.org/images/RNA2020-covers-DSSR.png)

I am so glad to know that you have found the DSSR-PyMOL approach much easier to use, and producing better schematics. In addition to the --cartoon-block option you mentioned, users may also want to try the --blocview option. It is the option used for pre-calculated results of PDB entries in http://skmatic.x3dna.org.

For viewers of this thread, I'd say that the supplemental PDF (http://skmatic.x3dna.org/gkaa426-supp.pdf) is well worth reading. In concluding the DSSR-PyMOL paper (https://doi.org/10.1093/nar/gkaa426), I wrote specifically:

Quote
Finally, all results reported here are completely reproduceable (see the supplemental PDF). Any questions related to this work are welcome and will be openly addressed on the 3DNA Forum (http://forum.x3dna.org).

Best regards,

Xiang-Jun