Eric Martz wrote: >In his announcement of 10.9.76, Bob asked for suggestions regarding the >dynamic popup menu. > >I would like to reiterate an old request. In Chime, the menu Select, >Residue lists all 20 amino acids, but grays out any not present in the >currently loaded PDB file. Thus, in 1D66, GLY, MET, and PHE are grayed out. >This makes it very easy to spot which amino acids are not present. It is a >very useful feature of Chime. > >At the end of the 20 amino acids are listed any other residues (group >names) that occur in the model. However, Chime has the bug that nucleotides >are not listed! > > > shall we count them, too?
ALA (3) ARG (2) ... etc? >1. My suggestion is that missing residues be listed (as they are now) but >grayed-out in Jmol's Select, Protein, By Residue Name list. > >2. Also, nucleotides absent should be grayed out in Select, Nucleic. > >3. There is a typographic error in Select, Nucleic: RNA is listed as ARN >(in 10.9.70). > > > I found that last week. It's gone >4. Since Jmol deems some non-standard (HETERO) residues to be protein, >these should be listed in Select, Protein, By Residue Name. I recommend >that non-standard residues be listed AFTER the 20 standard amino acids, and >separated from that list by a blank line. Thus in 1BKX, SEP and TPO would >be on the list. Similarly for non-standard nucleotides (tho I don't recall >how Jmol handles these). 1EVV has many non-standard nucleotides. > >5. Jmol's Select, Hetero, by HETATM menu is unpopulated (in 10.9.70). > > > that was because I was not entering anything there that did not have a HETNAM record -- but I've got Jmol reading the PDB HET record now as well. We'll see.... >6. I tried to get 10.9.76 but can't find it. Sourceforge lists only >10.9.75, nor did I spot it at Bob's server. > > > hmm. Bob ------------------------------------------------------------------------- Using Tomcat but need to do more? Need to support web services, security? Get stuff done quickly with pre-integrated technology to make your job easier Download IBM WebSphere Application Server v.1.0.1 based on Apache Geronimo http://sel.as-us.falkag.net/sel?cmd=lnk&kid=120709&bid=263057&dat=121642 _______________________________________________ Jmol-users mailing list [email protected] https://lists.sourceforge.net/lists/listinfo/jmol-users
