Re: [Jmol-users] problem with rockets

[Bob H. <ha...@st...>]

Part of the issue is that I corrected the calculation of the rocket 
position so that now it is PRECISELY along the core of the alpha helix. 
Prior to this, rockets went from an initial alpha carbon to a final one, 
and that was clearly skewing the axis of the rockets. (For example, 
compare 10.2 and 11.0 with

load xxxx.pdb
rockets on;trace on

That is, with spacefill and trace and rockets. I believe that in 11.0 
you will see that the rocket perfectly "cores" the trace, but in 10.2 we 
were way off. 

I'll be interested in what people come up with for a potential solution 
to this. Parameters include:

 1) it must have a defined color and size
 2) this size must be a GLOBAL value, not one specific to a group
 3) color could be assigned (a) globally, (b) based on the head of the 
trailing rocket, or (c) based on the tail of the leading rocket
 4) presumably, visibility would depend upon both rockets being visible.


Bob


Angel Herraez wrote:

>El 17 Dec 2006 a las 18:11, Bob Hanson escribió:
>
>  
>
>>I'm not certain this is a bug. When two rockets sections are adjacent, a 
>>recent bug fix correctly represents them as two separate rockets. 
>>    
>>
>
>Yes, I've seen this change happen along releases; now rockets are a 
>bit shorter so they don't touch/overlap as before.
>
>  
>
>>But 
>>since there is no intervening connection point, there is no "trace" to 
>>draw. If it's truly bothersome, there might be a way around this.
>>    
>>
>
>To me, the problem is that in this way there is no perception of a 
>continuous chain, the user will not see this is a single polypeptide 
>chain. Some kind of trace connection would be much better in my 
>opinion.
>
>What do others think?
>
>I´ve put a screenshot and demo at
>http://biomodel.uah.es/pruebas/jmol/rockets/
>
>
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