Re: [Jmol-users] query Jmol for number of atoms visible

[timothy d. <mol...@ma...>]

On 2005-01-08 (16:03) Miguel wrote:

>>>I think that you need to define exactly what you mean by 'visible'
>>>
>>>Q: Do you mean 'has a non-zero spacefill' ?
>>>
>>>select *; spacefill off; wireframe on
>>>
>>>Q: How many of these atoms are visible?
>>>
>>
>>hi Miguel,
>>
>>all of them. :-)
>
>Are you sure that is what you meant to say ...
>
yes.  I think.  no, yes.  wait.=20

all *bonded* atoms.  that's what I meant to say.  :-)



>>but must have some way to determine which of those atoms get
>>painted to the screen - does this make sense?
>
>Yes ... but we need to define what you mean by 'painted to the
>screen'
>
>If spacefill is turned off, then the atoms are not painted to the
>screen.
>
>>spacefill would be fairly easy to get - count the spheres.
>
>Agreed
>
>>wireframe seems trickier - does Jmol render the atom at all, or
>>just the bond cylinders?
>
>Only the bonds get drawn.
>
oh.  but I thought of a way to kludge around that, if necessary. include a =
"stealth" spacefill command along with a wireframe command, like this:

wireframe 0.2
spacefill 0.2

it won't work for backbone or cartoons, though.


>Not that I just implemented
>
>star on|off|{size}|percentage
>
>To support bonded atoms. One can say
>
>select *; spacefill off; wireframe; select !bonded; star 20%
>
neat!


>>for backbone and related formats, could one count the alpha carbons
>>(or phosphorus atoms)?
>>
>>how big is the tree that I'm barking up?  ;-)
>
>I suppose that it is not too bad.
>
>Q: Why do you want this?
>
I thought it would be a helpful feature to be able to report how much of a =
molecule is being examined, perhaps as something like a % value, or even a =
graphic. =20

"You are looking at 13% of this total molecule based on atom count."


something like that.  <shrug>

I also thought it might be helpful to a designer to track the number of ato=
ms shown by a particular molvis script, and be alerted to prune the pdb fil=
e accordingly.  saves network traffic.

if we could combine it with a way to report the atomnos of all "visible" at=
oms, why that would be cherry.  an online design interface smart enough to =
save a script, and also prune the pdb file to optimal size - commence saliv=
ation. :-)


regards,

tim
--=20
Timothy Driscoll
molvisions - see, grasp, learn.
<http://www.molvisions.com/>
usa:north carolina:wake forest

"I've had a perfectly wonderful evening. But this wasn't it." - Groucho Mar=
x