Samuel Flores wrote:
>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
>
>
select 1.1;spacefill on;wireframe off
>2. Hide the atoms of frame 1.
>
>
>3. Show the bonds between atoms in frame 1.
>
>
>
select 1.2;spacefill off;wireframe 0.05
4. show all the atoms in both frames
frame 0
>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..
>
>
>
Or, just have the initial atoms and only one frame and then:
draw line1 {0 0 0} {1 0 1}
draw line2 {1 0 1} {1 1 1}
etc.
or, perhaps:
draw square1 plane {0 0 0} {0 0 1} {0 1 1} {0 1 0}
draw square1 mesh nofill
>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:
>>>>
>>>>
>>>>
>>>>
>>>>
>>>>
>>>>
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>>>
>>>
>>--
>>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
>>
>>
>>
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>
>
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>
--
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
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