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.
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.
"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 atoms
shown by a particular molvis script, and be alerted to prune the pdb file
accordingly. saves network traffic.
if we could combine it with a way to report the atomnos of all "visible" atoms,
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 salivation. :-)
regards,
tim
--
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 Marx
-------------------------------------------------------
The SF.Net email is sponsored by: Beat the post-holiday blues
Get a FREE limited edition SourceForge.net t-shirt from ThinkGeek.
It's fun and FREE -- well, almost....http://www.thinkgeek.com/sfshirt
_______________________________________________
Jmol-users mailing list
[email protected]
https://lists.sourceforge.net/lists/listinfo/jmol-users
