> Thanks everyone. Angel I like your solution. I thought so. It's more logical and general.
> Why do we need both "protein" or "amino"? amino is rasmol-compatible. protein is Jmol chemical intelligence, particularly to account for funny cases like yours. Also, I think, it includes nonstandard-name residues (hetero) that are normal enough to be aa residues --or maybe I'm wrong. > In the code for FirstGlance, I enumerate all 20 > amino acid names in order to select protein atoms > that lack alpha carbons. "amino" is much easier! If I am interpreting it rigth, this is what Jmol source code says: (from http://jmol.svn.sourceforge.net/viewvc/jmol/trunk/Jmol/src/org/jmol/vi ewer/JmolConstants.java?view=markup) "@amino _g>0 & _g<=23" that is, "ALA", "ARG", "ASN", "ASP", "CYS", "GLN", "GLU", "GLY", "HIS", "ILE", "LEU", "LYS", "MET", "PHE", "PRO", "SER", "THR", "TRP", "TYR", "VAL", "ASX", "GLX", "UNK" "carbohydrate" is [AFL],[AGC],[AHR],[ARA],[ARB],[BDF],[BDR],[BGC],[BMA],[FCA],[FCB], [FRU],[FUC],[FUL],[GAL],[GLA],[GLB],[GLC],[GUP],[LXC],[MAN],[RAA], [RAM],[RIB],[RIP],[XYP],[XYS],[CBI],[CT3],[CTR],[CTT],[LAT],[MAB], [MAL],[MLR],[MTT],[SUC],[TRE],[ASF],[GCU],[MTL],[NAG],[NAM],[RHA], [SOR],[XYL] "protein" and "nucleic" are based on atom names AFAIK > Is a similar situation possible for nucleic? I don't think so. > is, is there one atom that is required in order > for other atoms in the same group to be deemed > "nucleic" (like alpha carbon for protein)? Probably P, I'm guessing. Deeper exploration of the source is needed to be sure. No, see the wiki link below > what would be the safe syntax to select ALL atoms > in standard nucleotides, regardless of atoms that may lack coordinates? Maybe use select A, G, C, T, U, DA, DG, DC, DT of course that misses unusual nucleotides (like inosine?) See also http://wiki.jmol.org/index.php/AtomSets (that's what I cold collate-infer some time ago) ------------------------------------------------------------------------------ The ultimate all-in-one performance toolkit: Intel(R) Parallel Studio XE: Pinpoint memory and threading errors before they happen. Find and fix more than 250 security defects in the development cycle. Locate bottlenecks in serial and parallel code that limit performance. http://p.sf.net/sfu/intel-dev2devfeb _______________________________________________ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
