On 18 Jul 2007 at 15:22, Eric Martz wrote: > As part of the PDB's remediation project ( > http://remediation.wwpdb.org/ ), they made changes to the PDB format, > now called version 3. Notably, DNA nucleotides are named DA, DT, DC, > DG, DI while RNA remain A, U, C, G, I.
Hello. I was also wondering what the "new V3" format would mean in practice, but had not read through any details. wwPDB documentation at http://remediation.wwpdb.org/software.html says literally: "...software tools that are compatible with the nomenclature that is used in PDB Version 3.0 (remediated) and PDB Version 3.1 (data released after August 1, 2007)." and the list includes "JMol V11.2.4" !!! > So far I have not managet personally to test the consequences of the > remediated PDB format e.g. for FirstGlance in Jmol. However, at least > the change in DNA naming seems likely to me to require changes within > Jmol itself. I have quickly tested a couple of files, 1asy.pdb (protein + RNA) and 1bna.pdb (DNA), in remediated format (gzipped), and they give no trouble in 11.2.4 For example, "select nucleic", "select dna" , "select rna" work in both. In 1bna, "select a" works, but "select [A]" selects nothing since the residues are named DA; "select [DA]" does work, same as "select a" "select t" does not work **this needs fixing**. "select dt" works ok "select backbone", "select sidechain", "select bases", "select purine", "select pyrimidine", "select cg" all work OK "select at" selects adenosines only **this needs fixing** probbaly because select t is not working (see above) "select au" does not work "select u" selects thymidines in DNA !! So, for the most part, I see that Jmol is taking care of this particular change. We need to make sure, though, that there aren't any other relevant changes in the format. ------------------------------------------------------------------------- This SF.net email is sponsored by: Microsoft Defy all challenges. Microsoft(R) Visual Studio 2005. http://clk.atdmt.com/MRT/go/vse0120000070mrt/direct/01/ _______________________________________________ Jmol-users mailing list [email protected] https://lists.sourceforge.net/lists/listinfo/jmol-users
