From: Carsten Olbrich (
Date: Thu Dec 10 2009 - 04:43:03 CST

Dear Dawn,
a colleague of mine has just sent me his latest version of a VMD script
to visualize conformational changes similar to the Porcupine plots of
Dynamite. As he has also mentioned to me, he would be happy to get any
response, if you can think of any further improvements or have any
In general, this script should not require further changes in the code
as long as there are no bugs. :)
The output should be a collection of arrows pointing from one state of
the selected atoms to the other, including the deviation color-coded and
indicated by the length. Hence, you can simply load the PCA trajectory
of the eigenvector and use the script to visualize the conformational

If you would be interested in really using this tool, he would be open
to sent you any new version, if any changes are required or wanted...

Best regards,


On Mon, Dec 7, 2009 at 1:49 PM, Joshua Adelman <> wrote:
> Hi Dawn,
> You can convert a dcd file to a trr file using catdcd which you can get off
> of the VMD/NAMD website. Then using trajconv which is a tool distributed
> with Gromacs, you can convert from a .trr to a .xtc file. There may be other
> tools that can go directly from .dcd to .xtc, but this is generally what I
> do.
> Josh
> On Dec 7, 2009, at 3:43 AM, Dawn wrote:
> Thank you for your response.  I will try and hope it works.
> I know Dynamite can do it, but needing xtc file instead of Charmm dcd file.
> I'll appreciate if you know the transition of dcd to xtc.
> Thank you!
> On Sun, Dec 6, 2009 at 11:22 PM, Joshua Adelman <> wrote:
>> Hi Dawn,
>> There is probably a fancy way to do it, but a quick and dirty method that
>> I've used is the following. If you have a series of conformations along the
>> mode, you can have VMD display all frames simultaneously in the 'Trajectory'
>> tab of the Representations GUI. I select the CA atoms and draw them in the
>> VdW representation. Play around with the size of the spheres so that they
>> overlap such that they look like a line or bar along the mode. You can color
>> them by the frame index for clarity. Create another selection where you show
>> the reference structure in whatever representation that you want.
>> Josh
>> On Dec 6, 2009, at 2:29 PM, Dawn wrote:
>> > Hi,
>> > I want to have porcupine plots for the first principal component
>> > PC1(derived from PCA). Would you please tell me if VMD have such function
>> > and how to do it?
>> >
>> > Thanks a lot!
>> > Dawn