Hello again I suspect this is an issue of different terminology, but the functionality you ask for is likely there.
Some pointers: http://chemapps.stolaf.edu/jmol/docs/#atomexpressionsfunctions see WITHIN SEQUENCE e.g. select within("PGATG",*) //would select all atoms in that peptide sequence > My work entails using the CHARMM simulation software where one of the ways to > select a portion > of the protein molecule entails using the "segid" command: e.g. select segid > PROA .and. .not. > resname TIP3). There is a similar issue with Amber software tools as well. Q: where is this PROA defined? > In addition, VMD, PyMol, and PDB format all allow selection on the segid > keyword. PDB is not a software -- what do you mean it allows selection? Jmol can also select segments of secondary structure, by number (order). I don't remember the syntax, but I'm quite sure I've seen it. Ah, there it is! Try this: load =1crn; show structure; // see the result in the console trace only; color trace group; selectionHalos on; //for better display select strucno=1; select strucno=2; select strucno=3; select strucno=4; documented at http://chemapps.stolaf.edu/jmol/docs/#atomproperties under "strucno" > canonical selection rules that coincide with the PDB formatting style. Again, where are those segments defined in the PDB file? ------------------------------------------------------------------------------ Master SQL Server Development, Administration, T-SQL, SSAS, SSIS, SSRS and more. Get SQL Server skills now (including 2012) with LearnDevNow - 200+ hours of step-by-step video tutorials by Microsoft MVPs and experts. SALE $99.99 this month only - learn more at: http://p.sf.net/sfu/learnmore_122512 _______________________________________________ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
