Hi Volker On 21 Sep 2008 at 13:56, Volker Blum wrote:
> 1) (minor) For two initially unconnected atoms, I cannot help much with this. From http://chemapps.stolaf.edu/jmol/docs/#connect it seems that you might need to specify "opaque" or "ModifyOrCreate" options for this to work. > 2) Regarding cartoons (ribbons etc) - I have found it excessively tedious to [...] > What exact information does jmol even require to safely produce a ribbon? For > me, this was a rather frustrating "guessing in the dark experience. You get a helix if there is a HELIX record in the PDB file, specifying the residue range. Alternatively, you may try "calculate structure" -- but that will likely nedd proper identification of Calpha and so on, not sure. http://chemapps.stolaf.edu/jmol/docs/#calculate There is also a rather undocumented feature in Jmol by which you can force a helix or sheet, using "calculate" command I think. I think this was described in a recent post in the email list, cannot find it now. Hey, there it is clearly documented! http://chemapps.stolaf.edu/jmol/docs/#structure > Is there any reason why a ribbon should not be producable by "simply" > specifying the atoms to be connected from within jmol itself? Having such a > feature available would be a great help .... That's "structure helix" !! This is why I love Jmol... On 21 Sep 2008 at 14:36, Volker Blum wrote: > as two additional points, > > - "Hbonds off" only turns off the last created H-bond in a structure, not the > others Not the last created bond, but all bonds in the currently selected atom set. > - The "Export -> image" menu as well as the "Save current view as an image" > button do not function in the "prerelease 11.6.RC15" version downloaded by me > today (I downloaded the binaries package, not the source). This used to work > without problems in 11.2.x (which I used before). There has been some redesign recently in the signed applet for this, so it may be that. If you get no answer from Bob, please open a bug report. > I may be reporting these things to the wrong list, but since this is an RC > version, I thought I'd do so anyway just in case. This is a perfect place. It could have gone into the developers list, but all users may benefit from the problems and the replies. ------------------------------------------------------------------------- This SF.Net email is sponsored by the Moblin Your Move Developer's challenge Build the coolest Linux based applications with Moblin SDK & win great prizes Grand prize is a trip for two to an Open Source event anywhere in the world http://moblin-contest.org/redirect.php?banner_id=100&url=/ _______________________________________________ Jmol-users mailing list [email protected] https://lists.sourceforge.net/lists/listinfo/jmol-users
