From: IJ (wenchangyu2006_at_gmail.com)
Date: Tue May 05 2009 - 10:16:45 CDT

Thank you, John. I tried volmap tool in VMD. And the the value for
"selection" is water, volmap type is density. Other values are default
values. But I still can not get the picture similar to STMV. Are there any
other parameters I have to modify?

Best,
Wenchang

2009/5/5 John Stone <johns_at_ks.uiuc.edu>

>
> Hi,
> The water box for STMV was created with the "volmap" command
> (or the GUI interface), with the "density" map type, if I recall.
> The surface of the capsid was generated via MSMS one fragment at
> a time, IIRC.
>
> Cheers,
> John Stone
> vmd_at_ks.uiuc.edu
>
> On Tue, May 05, 2009 at 09:31:33PM +0800, ?????? wrote:
> > Dear all,
> > Does anyone konw how to make images like STMV on VMD website?
> > (
> http://www.ks.uiuc.edu/Gallery/Science/Structure/tn/cover_fig_st.jpg.html<
> http://www.ks.uiuc.edu/Gallery/Science/Structure/tn/cover_fig_st.jpg.html>
> > )
> > I am very interested in making the water box and ions in this picture,
> which
> > is beautiful and proteins can be seen clearly.
> > Thank you.
> >
> > Best,
> > Wenchang
>
> --
> NIH Resource for Macromolecular Modeling and Bioinformatics
> Beckman Institute for Advanced Science and Technology
> University of Illinois, 405 N. Mathews Ave, Urbana, IL 61801
> Email: johns_at_ks.uiuc.edu Phone: 217-244-3349
> WWW: http://www.ks.uiuc.edu/~johns/ Fax: 217-244-6078
>