Re: [ccp4bb] DSSR-enabled innovative schematics of 3D nucleic acid structures with PyMOL

2020-05-23 Thread Xiang-Jun Lu
out the wrong link to nar/gkz1222 -- I was reading that interesting paper on 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://

[ccp4bb] DSSR-enabled innovative schematics of 3D nucleic acid structures with PyMOL

2020-05-23 Thread Xiang-Jun Lu
mental 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

[ccp4bb] 3DNA-DSSR annotated G-quadruplexes in the PDB (http://G4.x3dna.org)

2019-08-06 Thread Xiang-Jun Lu
Xiang-Jun Lu (Ph.D.) Email: xiang...@x3dna.org Web: http://x3dna.org/ Forum: http://forum.x3dna.org/ To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB&A=1

[ccp4bb] DSSR-enhanced visualization of nucleic acid structures in Jmol

2017-05-07 Thread Xiang-Jun Lu
(open access)](https://doi.org/10.1093/nar/gkx365) * [Details for reproducing reported results]( http://forum.x3dna.org/dssr-jmol-integration/) * [DSSR-Jmol manual](http://jmol.x3dna.org/dssr-jmol-manual.pdf) Best regards, Xiang-Jun [This message is posted on ccp4bb and pdb-l. Sorry for an extra copy of it you may receive.] -- Xiang-Jun Lu (PhD) Email: xiang...@x3dna.org Web: http://x3dna.org/ Forum: http://forum.x3dna.org/

[ccp4bb] Fwd: HETATM (.pdb) vs. ATOM (cif) records for modified nucleotides

2015-05-26 Thread Xiang-Jun Lu
cases I tested (e.g., 1s72, the Haloarcula Marismortui large ribosomal subunit). Has anyone on this list experienced similar issue? Thanks, -- Xiang-Jun PS. This is a slightly revised message initially sent to pd...@sdsc.edu on Friday, May 22. Xiang-Jun Lu (PhD) Email: xiang...@x3dna.org Web

[ccp4bb] DSSR v1.0.3 is released, and it has a user manual

2014-03-10 Thread Xiang-Jun Lu
ed problems are welcome on the form, and will be promptly addressed. [Posted to CCP4BB and the pdb-l mailing list on Monday, 2014-03-10] Xiang-Jun -- Xiang-Jun Lu (PhD) Email: xiang...@x3dna.org Web: http://x3dna.org/ Forum: http://forum.x3dna.org/

[ccp4bb] DSSR: Software for Defining the (Secondary) Structures of RNA

2013-03-11 Thread Xiang-Jun Lu
component of the 3DNA (http://x3dna.org/) suite of programs for the analysis, rebuilding, and visualization of three‐dimensional nucleic acid structures. -- Xiang-Jun Lu (PhD) Email: xiang...@x3dna.org Web: http://x3dna.org/ Forum: http://forum.x3dna.org/