Angel, could you please double check now and see if Jmol 11.2.5 works as you expect in this regard?
translations needed for the new "Identity" menu item. Bob Angel Herraez wrote: >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 > > -- Robert M. Hanson Professor of Chemistry St. Olaf College Northfield, MN http://www.stolaf.edu/people/hansonr If nature does not answer first what we want, it is better to take what answer we get. -- Josiah Willard Gibbs, Lecture XXX, Monday, February 5, 1900 ------------------------------------------------------------------------- This SF.net email is sponsored by: Splunk Inc. Still grepping through log files to find problems? Stop. Now Search log events and configuration files using AJAX and a browser. Download your FREE copy of Splunk now >> http://get.splunk.com/ _______________________________________________ Jmol-users mailing list [email protected] https://lists.sourceforge.net/lists/listinfo/jmol-users
