Dear Bob, I have now done some tests on nucleic acids for the old vs. new PDB formats. The old format, version 2.3, has been in effect since 1998. The new "remediated" version goes into effect August 1, 2007. Differences are summarized in http://www.wwpdb.org/documentation/format3.1-20070719.pdf
In my tests, unless otherwise noted, I used Jmol 11.3.6. ----------------------- 1. BUG: "select dna" select DNA or RNA: "select dna" seems to me to have a bug: it selects rna as well as dna. A good test PDB file is 104D (PDB new format 3), which has both (510 DNA atoms and 256 RNA Atoms). So, in 104D, "select dna" selects 766 atoms, surely not the desired behavior. This bug was NOT PRESENT in Jmol 10.2.0 (still in use in the main public FirstGlance in Jmol version 1.0), but WAS PRESENT in Jmol 11.1.27 as well as in Jmol 11.3.6. ---------------------- 2. OK: "select t" selects thymidine in 104D (128 atoms). "select [t]" selects 0 atoms, which seems correct since thymidine now has the group name DT. "select dt" and "select [dt]" both work (128 atoms). ---------------------- 3. ??: Things get more problematic with "select a,c,g" because these select both DNA and RNA. Now that DNA residues are named DA, DC, and DG, is this the desired behavior? Tests with 104D: "select g" gets 270 atoms, including both DNA and RNA guanosines. "select [g]" gets only 136 atoms, the RNA G atoms, confirmed with "select rna and [g]". This is correct because the DNA G atoms are named DG. "select [dg]" or "select dg" gets 134 atoms (DNA G). "select [dg],[g]" gets the same as "select g", 270 atoms (DNA G + RNA G). However, since "select dna" gets all RNA, "select dna and [g]" gets the 136 RNA G atoms. ---------------------- 4. BUGS? Using 1EVV (new PDB format) in Jmol 11.3.6, there are some things I don't understand. "select 2mg" selects [C2]:A and [HOH]2, but not the one residue named 2MG. "select [2mg]" correctly selects the latter, [2MG]10:A. "select 5mu" behaves similarly. "select [5mu] and 5mu" gets 0 atoms, consistent with the above (buggy?) behavior. However, reversing the order, "select 5mu and [5mu]" generates an error, as does also "select 5mu and rna" script compiler ERROR: end of expression expected -------------------------- -------------------------- I think I've found some additional anomalies but I need to do more testing to be sure. More on those later, if I can confirm them. -Eric ------------------------------------------------------------------------- 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
