On 6 Apr 2009 at 20:25, Karol Jarolimek wrote:
> I think the "connect {*} {*} delete" command has to be there
> otherwise jmol will not update the bonds i.e. bonds do not break.
I'm afraid I don't follow this. Which bonds must be broken?
I'm still not sure why you need to use the callback, rath
(Apologies if you receive duplicated posts; my email server has gone nuts
last week)
On 6 Apr 2009 at 20:25, Karol Jarolimek wrote:
> I think the "connect {*} {*} delete" command has to be there
> otherwise jmol will not update the bonds i.e. bonds do not break.
I'm afraid I don't follow this.
oh, yes, that might be right. Definitely connect {*} {*} delete has to be
there.
Well, you have to expect some sort of delay for the calculation
On Mon, Apr 6, 2009 at 1:25 PM, Karol Jarolimek
wrote:
> I think the "connect {*} {*} delete" command has to be there
> otherwise jmol will not upd
I think the "connect {*} {*} delete" command has to be there
otherwise jmol will not update the bonds i.e. bonds do not break.
I tried the version 11.7.31 but the flickering remains.
Might be also due to the size of the system ...
-
I thought I fixed that in the very latest versions of Jmol. Are you using
that? I think the refresh true/false doesn't work with animation in the
older versions.
On Sat, Apr 4, 2009 at 1:48 PM, Angel Herráez wrote:
> > However when I run the animation the screen
> > starts to flicker.
>
> I t
> However when I run the animation the screen
> starts to flicker.
I think that deleting all bonds at each frame may be time-consuming and might
also cause
the flickering.
You don't need "connect {*} {*} delete" if you use "set autobond off" before
loading.
Try that
-
I tried this script:
function setConnections
set refreshing false
connect {*} {*} delete
connect 1.79 (_Si) (_H);
connect 2.16 (_Si) (_N);
connect 0.90 (_H) (_H);
connect 1.18 (_H) (_N);
connect 1.20 (_N) (_N);
set refreshing true
end function
load TRAJECTORY myfil
The faster way would be to load the file with the keyword TRAJECTORY. This
allows far faster select and connect processes, because only 370 atoms, not
370x500 will be present at a given time. But then you need that connect
command set in a frame change callback so that it can run every time you get
OK I used the connect command and it works like
a charm. I open the XYZ file and then load the script:
set autobond false;
connect 2.65 (_Si) (_Si);
connect 1.79 (_Si) (_H);
connect 2.16 (_Si) (_N);
connect 0.90 (_H) (_H);
connect 1.18 (_H) (_N);
connect 1.20 (_N) (_N);
I think Jmol loops over a
It can be done with the frame callback method, but it seems we don't
need to go that way. Based on my quick test, the connect command
works for all frames in one go without trouble, and the redefined
bonds are kept across the animation.
So, you may just need to disable autobonding and then apply
Karol, I think what Bob suggested is
1. there is no implementation of custom covalent radii
2. you can use the "connect" command to substitute for that: have
Jmol calculate and render bonds base on your radii
3. you must do that for each and every frame in your
animation/dynamics
The callback is
I am sorry, I do not follow completely...
What do you mean by "frame change callback" ?
Do I have to use the "connect" command and after that
the "animation" command at each molecular dynamics step ?
I am new to Jmol, so some example script would be of
a great help.
And what about the user define
I think you may need to use a frame change callback. You can have it
running a jmol script function that uses the connect command. It will
slow down the animation, but should work.
Sent from my iPhone
On Mar 22, 2009, at 2:56 AM, k.jaroli...@science.ru.nl wrote:
> Hi,
>
> I am trying to vi
Hi,
I am trying to view a molecular dynamics simulation, where bonds are being
formed and destroyed. The data is in the XYZ format containing multiple
structures. However I would like to use my own cut-off distances for
bonds.
Is there a way to do this in Jmol ?
Are the bonds being evaluated at ea
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