Yes ! I'm finally on Jmol's cutting edge !
Here is my report :
- no more gliding spiders with Bob's last version !
- when a chain contains gaps the different pieces are split by the dragging
process (for example : 1qln, 2bg9)
- to make chains go back to where they came from, I had to store the
coordinates for each chain in a variable. It doesn't work if I use the
coordinates for the whole model. eg :
- "tempset ={*}.xyz.all" then move the chains around, "rotate compare
{*} @tempset -2", makes a rotation of the whole scene but not of the different
chains relative to each others.
-"tempset={*a}.xyz.all", then move the chain A around, "rotate compare
{*a} @tempseta -2"; makes a cool motion of the chain A back to where it came
from. There is a problem though with solvent molecules (PDB ID 1gzx for
example), where the solvent molecules are not moved when the chain with the
same ID is dragged, but are moved when the rotate compare command is issued. To
prevent that, I had to change slightly the atoms set : "tempset={*a and not
solvent}.xyz.all" ; "rotate compare {*a and not solvent} @tempseta -2}
It works great, even if the scene has been rotated.
So, to use this feature it is required to store for each chain the initial
coordinates as soon as the set picking dragmolecule command is issued. There is
a question regarding the solvent : should it be included with the rest of the
chain in the dragging process ?
Finally, I think it's a great tool for exploring complex molecules : you can
imagine students pulling chains apart in order to study some other chains (as
for display or restrict commands, but in an interactive manner). It could be
great also as a teaching tool to introduce proteins quaternary structure. (plus
many other applications !)
-Paul
Le 9 mai 2011 à 06:16, Robert Hanson a écrit :
> You need to store them in a variable at some point before you start moving
> things. Really, Paul, you are among the first to experiment with this, so
> understand that it could be trickier than I make it out to be!
>
> On Sun, May 8, 2011 at 3:29 PM, Paul Pillot <[email protected]>
> wrote:
> It works great now ! Thanks Bob !
> You mentioned in one of your previous messages that one can use the ROTATE
> COMPARE command to move the chains smoothly back to where they came from.
> I've seen in the docs that the ROTATE COMPARE command requires the
> coordinates from the previous position to be stored (eg : {2.1}.all.xyz).
>
> I think that's {2.1}.xyz.all -- xyz coordinates (all of them, as an array,
> not just the average). The "smooth change" would require that you have the
> coordinates specifically of the atoms that have been moved. In my case, I was
> moving the first model in the second file. So I saved just those coordinates.
> Might be tricky to set this up with any atoms the user moves. You can always
> get them back, but not necessarily smoothly. For that we might need a new
> "morph" command.
>
> Bob
>
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