VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Wed Apr 05 2006 - 12:32:49 CDT

Hi,
  I didn't get the attached picture in the email you sent.
If you're having trouble with Surf, you might try MSMS instead:
  http://www.scripps.edu/~sanner/html/msms_home.html

There are some structures that neither Surf nor MSMS will be able
to process correctly. If you're just looking for a coarse graphical
representation (and not an actual solvent accessible surface) for
this large 58,000 atom structure, you might prefer to use the
Extensions->Analysis->VolMap tool in VMD 1.8.4 to produce a surface
representation at a user-selected resolution, rather than using Surf/MSMS.

  John Stone
  vmd_at_ks.uiuc.edu

On Wed, Apr 05, 2006 at 03:14:55PM +0530, M.S.Vijayabaskar wrote:
> Hi,
> The SURF representation is not proper when I render it for the protein
> 1AON.pdb
> The protein has some 58000 odd atoms and the computer after quite sometime
> gives me a improper picture ..... I have attached a picture for your
> reference.
>
> I work on - Mandriva 10.x Linux with kernel details
> -----------------------------------------------
> 2.6.12-12mdksmp #1 SMP Fri Sep 9 17:43:23 CEST 2005 i686 Intel(R)
> Pentium(R) 4 CPU 3.00GHz unknown GNU/Linux
> -----------------------------------------------
>
> I use a nvidia geforce fx 5200 with 128 memory AGP card.
>
> Could you please tell me the solution to this problem !
>
>
>
> --
> Victory goes to the player who makes the next-to-last mistake -
> Chessmaster Savielly Grigorievitch Tartakower (1887-1956) 

-- 
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