VMD-L Mailing List

From: Anton Arkhipov (anton_at_ks.uiuc.edu)
Date: Tue May 05 2009 - 12:48:10 CDT

Hi Wenchang,

Actually, I made that image using MSMS for the water box, setting
material to transparent. That makes a nicely looking box. But, you
definitely should be able to use volmap. You can try to vary the
volmap parameters a bit, say, using 3 or 5 A resolution, and 3 or 5 A
atom size. Also, for selection in volmap you don't have to use "water"
- you can use "all", then the box will be more uniform inside.

As to the virus capsid, I indeed used MSMS. I had to use MSMS there
for a few overlapping selections (each about a quarter to a third of
the capsid). So, you don't have to render each protein unit in MSMS
separately.

Best,

Anton.

On 5 May 2009, at 10:16, 周文昌 wrote:

> 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
>