It seems to me that it is not a bug if Jmol correctly selects [DA] and [A] for group names. In addition, "select a" correctly selects for adenine, regardless of its naming. That is correct as well. That is because not all adenines are named "A" even in the standard PDB database.
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" > > > not a bug. "select [DA]" is NOT the same as "select a", nor is "select [A]" the same as "select a". >"select t" does not work **this needs fixing**. "select dt" works ok > > > This must be fixed. "select t" currently selects for nucleic groups having a C5M atom based on the likes of: ATOM 126 P T A 7 8.081 14.050 11.915 1.00 40.72 1BNA 188 ATOM 127 O1P T A 7 8.600 12.894 11.137 1.00 42.53 1BNA 189 ATOM 128 O2P T A 7 6.668 13.960 12.342 1.00 46.75 1BNA 190 ATOM 129 O5* T A 7 8.239 15.387 11.076 1.00 35.21 1BNA 191 ATOM 130 C5* T A 7 7.907 16.635 11.686 1.00 34.88 1BNA 192 ATOM 131 C4* T A 7 8.162 17.628 10.598 1.00 31.45 1BNA 193 ATOM 132 O4* T A 7 9.543 17.580 10.279 1.00 46.82 1BNA 194 ATOM 133 C3* T A 7 7.461 17.284 9.296 1.00 23.76 1BNA 195 ATOM 134 O3* T A 7 6.251 18.034 9.162 1.00 44.27 1BNA 196 ATOM 135 C2* T A 7 8.532 17.527 8.223 1.00 26.30 1BNA 197 ATOM 136 C1* T A 7 9.644 18.209 9.019 1.00 28.96 1BNA 198 ATOM 137 N1 T A 7 11.021 17.903 8.565 1.00 20.47 1BNA 199 ATOM 138 C2 T A 7 11.822 18.923 8.176 1.00 28.01 1BNA 200 ATOM 139 O2 T A 7 11.383 20.077 8.143 1.00 40.01 1BNA 201 ATOM 140 N3 T A 7 13.119 18.641 7.852 1.00 27.94 1BNA 202 ATOM 141 C4 T A 7 13.633 17.372 7.882 1.00 15.14 1BNA 203 ATOM 142 O4 T A 7 14.830 17.222 7.619 1.00 32.54 1BNA 204 ATOM 143 C5 T A 7 12.781 16.325 8.235 1.00 10.83 1BNA 205 ATOM 144 C5M T A 7 13.269 14.902 8.236 1.00 36.33 1BNA 206 ATOM 145 C6 T A 7 11.465 16.616 8.594 1.00 12.19 1BNA 207 in the remediated files, this is now: ATOM 122 P DT A 7 8.081 14.050 11.915 1.00 40.72 P ATOM 123 OP1 DT A 7 6.668 13.960 12.342 1.00 46.75 O ATOM 124 OP2 DT A 7 8.600 12.894 11.137 1.00 42.53 O ATOM 125 O5' DT A 7 8.239 15.387 11.076 1.00 35.21 O ATOM 126 C5' DT A 7 7.907 16.635 11.686 1.00 34.88 C ATOM 127 C4' DT A 7 8.162 17.628 10.598 1.00 31.45 C ATOM 128 O4' DT A 7 9.543 17.580 10.279 1.00 46.82 O ATOM 129 C3' DT A 7 7.461 17.284 9.296 1.00 23.76 C ATOM 130 O3' DT A 7 6.251 18.034 9.162 1.00 44.27 O ATOM 131 C2' DT A 7 8.532 17.527 8.223 1.00 26.30 C ATOM 132 C1' DT A 7 9.644 18.209 9.019 1.00 28.96 C ATOM 133 N1 DT A 7 11.021 17.903 8.565 1.00 20.47 N ATOM 134 C2 DT A 7 11.822 18.923 8.176 1.00 28.01 C ATOM 135 O2 DT A 7 11.383 20.077 8.143 1.00 40.01 O ATOM 136 N3 DT A 7 13.119 18.641 7.852 1.00 27.94 N ATOM 137 C4 DT A 7 13.633 17.372 7.882 1.00 15.14 C ATOM 138 O4 DT A 7 14.830 17.222 7.619 1.00 32.54 O ATOM 139 C5 DT A 7 12.781 16.325 8.235 1.00 10.83 C ATOM 140 C7 DT A 7 13.269 14.902 8.236 1.00 36.33 C ATOM 141 C6 DT A 7 11.465 16.616 8.594 1.00 12.19 C note the significant number of atom name changes. In particular, C5M has been relabeled "C7". This is probably fixable by allowing for C7 OR C5M, but that is not a trivial fix. Is there a full list of the remediated atom name changes? Bob >"select au" does not work > > > "select au" does not exist. >"select u" selects thymidines in DNA !! > > > because "select t" is not working in that particular case. > >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
