VMD-L Mailing List

From: Bogdan Costescu (bcostescu_at_gmail.com)
Date: Wed Nov 02 2011 - 13:42:01 CDT

Dear Axel and John,

Thank you for your suggestions. I have tried already Axel's and I
didn't see much improvement in speed, but after trying John's I have
understood that the speed limitation is coming from the cutoff
calculations and not from the graphical representation. I'll combine
this with a selection such that only the interesting regions are shown
with dynamics bond determination while the rest uses normal Lines -
this should make it quite a lot faster; it's nice that one could set
this per representation per molecule. Even though the dynamics bond
cutoff is not exposed in the GUI, it's fine for me: I have asked for a
quick-and-dirty way and got exactly that :-)

Thanks again!
Bogdan

On Mon, Oct 31, 2011 at 22:18, John Stone <johns_at_ks.uiuc.edu> wrote:
> Hi,
>  Actually there is an undocumented way of causing the lines representation
> to use a dynamic bond search, by setting the representation from a Tcl
> command, adding an extra parameter to set the cutoff distance for the
> bond search.  I have been meaning to add this to the GUI, but it will
> require significant changes to graphical representations window, so
> I have been waiting until several new features are exposed in the GUI
> at the same time ... but I digress.  To enable dynamic bond determination
> for the lines rep (and several others), just add the cutoff distance
> as an extra representation parameter.  For the lines rep you would normally
> have a representation command similar to this:
>  mol modstyle 0 0 Lines 1
>
> To cause it to use dynamic bond determination, add the cutoff, e.g. 1.6A
>  mol modstyle 0 0 Lines 1 1.6
>
> Cheers,
>  John Stone
>  vmd_at_ks.uiuc.edu
>
> On Mon, Oct 31, 2011 at 03:32:47PM -0400, Axel Kohlmeyer wrote:
>> On Mon, Oct 31, 2011 at 2:21 PM, Bogdan Costescu <bcostescu_at_gmail.com> wrote:
>> > Dear vmd-l,
>> >
>> > I would like to have some kind of DynamicBonds representation, but
>> > where the bonds are not represented as cylinders but as Lines. I like
>> > how DynamicBonds works, but the representation is slow because there
>> > are many cylinders to be drawn. Is there a quick-and-dirty way of
>> > combining the two ? I could, of course, just draw the lines myself
>>
>> no. at least not without changing source code
>> and building your own version of VMD.
>>
>> > from TCL for each frame, but again due to speed reasons I would prefer
>> > to use a built-in mechanism.
>>
>> you can reduce the cylinder resolution to 2 or 3 and diameter to 0.1
>> depending on your graphics hardware, turning GLSL on or off might
>> speed up things, too.
>>
>> axel.
>>
>> > Thanks in advance for any suggestion!
>> > Bogdan
>> >
>>
>>
>>
>> --
>> Dr. Axel Kohlmeyer
>> akohlmey_at_gmail.com  http://goo.gl/1wk0
>>
>> College of Science and Technology
>> Temple University, Philadelphia PA, USA.
>
> --
> NIH Resource for Macromolecular Modeling and Bioinformatics
> Beckman Institute for Advanced Science and Technology
> University of Illinois, 405 N. Mathews Ave, Urbana, IL 61801
> http://www.ks.uiuc.edu/~johns/           Phone: 217-244-3349
> http://www.ks.uiuc.edu/Research/vmd/       Fax: 217-244-6078
>