Date: Thu Dec 10 2009 - 05:24:12 CST

Dear All,

Have a nice day. Is there any way I can calculate the Surface Area/Volume of a protein cavity in VMD.

I have tried Caver in pyMol and it is a good tool for visualisation, but I am unable to quantify the cavity volume or surface area.

Anybody have experience in this area please suggest me something


On 10 Dec 2009, at 10:43, Carsten Olbrich wrote:

> 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
> questions.
> 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
> changes.
> 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,
> Carsten
> 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
> <PorcupinePlot.tcl>