Dear Robert,
Thank You very much, now the tip is moving.
Just I would like to ask you another question related to that please, after I
did the movement of the tip as you taught me, I wrote in the console (write
output.xyz) the file is saved but when I open it again in Jmol, the Si (Silicon
substrate) disappear. Jmol just showing me the tip only without the silicon
substrate. My question is
How to save the whole structure in (xyz format)? which means I need to save a
file including the Silicon substrate and tip after the new coordinates and the
movement of the tip?
Many thanks,RajabDate: Wed, 4 Jun 2014 21:13:23 -0500
From: [email protected]
To: [email protected]
Subject: Re: [Jmol-users] FW: (Set picking dragmolecule) problem
I think you are just running into memory issues. You can reduce those by:
set autobond false
set preservestate false
set allowMoveAtoms true
then use
select _C
set dragselected
and use alt-shift-left-drag.
I did this, and the carbon tip moved quite smoothly.
Bob
On Wed, Jun 4, 2014 at 4:54 PM, Eng.Rajab Al-Sayegh <[email protected]>
wrote:
Dear Jmol users and developers,
As for the attached file that could be found here
https://www.dropbox.com/s/z5v4zd2kcyx047l/output.xyz
there are two types of atoms: Carbon tip (represented as a ball) and Silicon
substrate.
What I just want to do to the structure, is to move the whole ball (the set of
Carbon atoms) at once, without causing the substrate to move.
I have done it plenty of times before for smaller structure, simply by choosing
the function (drag molecule) or by typing (set picking dragmolecule) in the
console and move the simple structure.
for some unknown reason, the function (set picking dragmolecule) does not work
with the attached structure when I'm trying to move the Carbon atoms (the whole
ball) at once.
I don't really know whither this problem is due to the file contents (large
structure) or Jmol limitation.
Please assist me with how to tackle this issue to move that ball.
Regards,Rajab
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