Hi Guys, I wonder if someone could tell me the right sequence of commands to solve a problem I'm having. The description follows.
I have a pdb file with the following frames: frame 0: atoms frame 1: pseudo-"atoms" and CONECT records, the purpose of which is to make rectangular cells around interesting regions of frame 0. I would like to do the following: 1. Show the atoms in frame 0 as spheres 2. Hide the atoms of frame 1. 3. Show the bonds between atoms in frame 1. The bonds in frame 1 will make the boxes to enclose and draw attention to regions of frame 0. I am having trouble figuring out how to select based on frame.. Many thanks Sam On Aug 30, 2007, at 1:23 PM, Bob Hanson wrote: > sorry -- two mistakes there; I only identified the first. It should > be: > > lcaocartoon o1 scale 1.2 color orange create "s" > color $o1s blue > > > because you have to designate both the identifier (o1) and the lobe > designation (s or pza or pzb, sp3a, sp3b, etc) in the color command. > > > > William Reusch wrote: > >> Bob, >> >> Unless I'm missing something, your sensible suggestion does not >> work. >> I am using a simple case in which only one orbital is created and >> named >> o1, e.g. >> lcaocartoon scale 1.2 color orange o1 create "s" >> Following this with the command >> color $o1 blue >> has no effect and gives a Jmol error message 'ScriptException object >> name expected after "$"'. >> >> Bill >> >> Bob Hanson wrote: >> >> >> >>> Bill, there was a bug in this regard that I fixed, but it involved >>> modifying the default LCAO names. >>> I'll change that page to indicate this. >>> >>> The thing to do is to give the lcaocartoons IDs and then refer to >>> them >>> using this id along with the specific lobe you want to address: >>> >>> lcaocartoon c3 create "pz" >>> >>> color $c3pza translucent white >>> color $c3pzb blue >>> >>> Bob >>> >>> >>> William Reusch wrote: >>> >>> >>> >>> >>> >> >> >> --------------------------------------------------------------------- >> ---- >> This SF.net email is sponsored by: Splunk Inc. >> Still grepping through log files to find problems? Stop. >> Now Search log events and configuration files using AJAX and a >> browser. >> Download your FREE copy of Splunk now >> http://get.splunk.com/ >> _______________________________________________ >> Jmol-users mailing list >> [email protected] >> https://lists.sourceforge.net/lists/listinfo/jmol-users >> >> > > > -- > Robert M. Hanson > Professor of Chemistry > St. Olaf College > Northfield, MN > http://www.stolaf.edu/people/hansonr > > > If nature does not answer first what we want, > it is better to take what answer we get. > > -- Josiah Willard Gibbs, Lecture XXX, Monday, February 5, 1900 > > > > ---------------------------------------------------------------------- > --- > This SF.net email is sponsored by: Splunk Inc. > Still grepping through log files to find problems? Stop. > Now Search log events and configuration files using AJAX and a > browser. > Download your FREE copy of Splunk now >> http://get.splunk.com/ > _______________________________________________ > Jmol-users mailing list > [email protected] > https://lists.sourceforge.net/lists/listinfo/jmol-users ------------------------------------------------------------------------- This SF.net email is sponsored by: Splunk Inc. Still grepping through log files to find problems? Stop. Now Search log events and configuration files using AJAX and a browser. Download your FREE copy of Splunk now >> http://get.splunk.com/ _______________________________________________ Jmol-users mailing list [email protected] https://lists.sourceforge.net/lists/listinfo/jmol-users
