VMD-L Mailing List

From: wenchangyu2006_at_gmail.com
Date: Sat Jan 02 2010 - 16:00:44 CST

Thanks Axel, John. I will present here what I have done to make the line,
although I'm not sure whether it is correct or not.
Anyway, in order to make the line, I do the following steps in Tk console:
Step 1, make a selection for the atoms I want to draw the line
% set A [atomselect top "segname PROA"];

Step 2, measure the interia for the selection
% measure interia $A
(In this step, the following information will come out: center of mass:
{xyz} and vector of the largest moment of inertia for the corresponding
selection: {{a1 b1 c1} {a2 b2 c2} {a3 b3 c3}} )

Then I think the line in direction1 will be the one from (x,y,z) to
(a1,b1,c1), and so are the lines in direction2 and direction3.

Step 3, use the command ""draw line point1 point2" or "draw cylinder point1
point2". The color can be modified to red by using command like "draw color
red", for example.
draw color red
draw cylinder {xyz} {a1 b1 c1} redius 0.5
draw cylinder {xyz} {a2 b2 c2} redius 0.5
draw cylinder {xyz} {a3 b3 c3} redius 0.5

Done!

Axel & John, am I right?


Best,
Wenchang

2010-1-2ÉÏÎç7:43£¬John Stone <johns_at_ks.uiuc.edu>׫д£º



> Hi,


> You can draw any lines or arrows you like using the VMD "graphics"


> or "draw" commands. The people that made the image you referred to


> long ago graduated and have since moved on to other institutions,


> but the key point is just that they wrote scripts that computed the


> line/cylinder endpoints and added them to their molecular rendering to


> help illustrate the change in orientation over time.





> Cheers,


> John Stone


> vmd_at_ks.uiuc.edu








> On Fri, Jan 01, 2010 at 12:28:22PM +0000, wenchangyu2006_at_gmail.com wrote:


> > Thank you, axel. Actually the picture on the webiste is exactly the one
> I


> > want to make. I searched the user guide about "inertia tensor"
> measurement


> > and I think I know how to draw a line in VMD. But I really don't know
> how


> > to transfer the information from inertia to draw the line. I think there


> > should be someone in UIUC made the picture when they put the picture on


> > the website. Thank you for any suggestion.


> >


> > Best,


> > wenchang


> >


> > 2010-1-1EIIc,12:57-L-NOTAxel Kohlmeyer akohlmey_at_gmail.com> *

> > > please always keep the mailing list in cc: so that


> > >


> > >


> > > people on the list get to see, if a request has been


> > >


> > >


> > > answered sufficiently or not.


> > >


> > >


> > >


> > >


> > >


> > > 2009/12/31 wenchangyu2006_at_gmail.com>:


> > >


> > >


> > > > Thank you, axel. Actually I would like to how to draw the lines in


> > that


> > >


> > >


> > > > picture on the website. I think this is the direction of the protein


> > moving


> > >


> > >


> > > > and this can be done by script programming, which I want to know.


> > Thanks.


> > >


> > >


> > >


> > >


> > >


> > > if you want to know about those lines, why don't you ask about it in


> > >


> > >


> > > the first place. please keep in mind that an answer to a question can


> > >


> > >


> > > only be as good and accurate as the question itself.


> > >


> > >


> > >


> > >


> > >


> > > those lines look like some position vectors of the principal axis to
> me


> > >


> > >


> > > that were derived from the inertia tensor at different time steps,
> where


> > >


> > >


> > > the color encodes the time.


> > >


> > >


> > >


> > >


> > >


> > > of course that can be scripted. again, please see the user's guide


> > (graphics


> > >


> > >


> > > commands). since this kind of imagery cannot be easily generalized,


> > you'll


> > >


> > >


> > > have to sort out the details by yourself.


> > >


> > >


> > >


> > >


> > >


> > > cheers,


> > >


> > >


> > > axel.


> > >


> > >


> > >


> > >


> > >


> > > > 2009-12-31IAIc,10:08-L-NOTAxel Kohlmeyer akohlmey_at_gmail.com>


> > *

> > >


> > >


> > > >> On Thu, Dec 31, 2009 at 6:47 AM, O:U:IA:^2y
> wenchangyu2006_at_gmail.com>


> > wrote:


> > >


> > >


> > > >>


> > >


> > >


> > > >>


> > >


> > >


> > > >> > Hi,


> > >


> > >


> > > >>


> > >


> > >


> > > >>


> > >


> > >


> > > >> > Does anybody know how to make the example on VMD website, titled


> > >


> > >


> > > >>


> > >


> > >


> > > >>


> > >


> > >


> > > >> > "Superposition of Multiple Trajectory Timesteps " in the
> following


> > link?


> > >


> > >


> > > >>


> > >


> > >


> > > >>


> > >


> > >


> > > >> >
> http://www.ks.uiuc.edu/Research/vmd/allversions/repimages/#examples


> > >


> > >


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> > > >> >


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> > > >>


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> > >


> > > >>


> > >


> > >


> > > >> > I appreciate if anybody can give some suggestions, thank you and


> > Happy


> > >


> > >


> > > >> > New


> > >


> > >


> > > >>


> > >


> > >


> > > >>


> > >


> > >


> > > >> > Year


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> > > >>


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> > > >>


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> > > >>


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> > > >> how about reading the VMD user's guide?


> > >


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> > > >> particularly the part about the contents of the


> > >


> > >


> > > >>


> > >


> > >


> > > >>


> > >


> > >


> > > >> trajectory tab in the graphical representations dialog.


> > >


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> > > >> cheers,


> > >


> > >


> > > >>


> > >


> > >


> > > >>


> > >


> > >


> > > >> axel.


> > >


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> > > >> --


> > >


> > >


> > > >>


> > >


> > >


> > > >>


> > >


> > >


> > > >> Dr. Axel Kohlmeyer akohlmey_at_gmail.com


> > >


> > >


> > > >>


> > >


> > >


> > > >>


> > >


> > >


> > > >> Institute for Computational Molecular Science


> > >


> > >


> > > >>


> > >


> > >


> > > >>


> > >


> > >


> > > >> College of Science and Technology


> > >


> > >


> > > >>


> > >


> > >


> > > >>


> > >


> > >


> > > >> Temple University, Philadelphia PA, USA.


> > >


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