Hi Angel, thanks!!
On Sunday 21 September 2008 15:23, Angel Herráez wrote: > 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. I see. In general, would it be helpful to have the appropriate default be "ModifyOrCreate" right away (if someone specifies a Hbond, this will most likely be the intention anyway) > > 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. hm ... I have such a record; I guess jmol misinterprets my pdb file for some reason (the reason may be that it's hand-edited and maybe does not conform to something jmol expects in some subtle way, so the issue here is perhaps more how to debug a pdb file to make it work for jmol - my problem, I guess) > 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 yes,that would seem t be exactly what I need. Comments: - the help text for structure is a literal copy of the "subset" explanation immediately below - the sequence of commands structure HELIX (atomno=17,18,19,27,28,29,37,38,39,47,48,49); ribbon on does nothing at all in my case (those are the numbers of the backbone ...-CCN-CCN-...'s . The whole thing is clearly helical - what am I missing?) Thanks for your help, and sorry about the perhaps silly follow-up questions. best, Volker > > 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 ------------------------------------------------------------------------- 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
