VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Tue Dec 28 2004 - 10:46:02 CST

Hi guys,
  I suspect you've triggered one of the bugs in Surf by sending it
such a large surface. My only suggestion would be to separately
calculate surfaces for the virus components. Virus structures seem
to cause problems for both Surf and MSMS in the tests I've done previously,
and the only way I was personally able to get either program to behave
well was to separately calculate surfaces for the various identical
subunits in the virus. I made an MSMS surface for a virus of the same
size you're trying by creating 60 MSMS reps, one for each piece of
the virus. That will work, but you will end up with a very very large
collection of triangulated geometry, so I hope you have a fast video card.

  John Stone
  vmd_at_ks.uiuc.edu

On Tue, Dec 28, 2004 at 05:14:27PM +0100, Axel Kohlmeyer wrote:
>
> >>> "DB" == dieter blaas <dieter.blaas_at_univie.ac.at> writes:
>
> DB> Thanx, Axel,
> DB> I had acidentially deleted the H:/temp directory which was defined as
> DB> environment variable. After I created it again, VMD made surfaces of
> DB> small molecules without trouble. However, when I try to render the
> DB> surface of the virus with roughly 400 000 coordinates I receive the
> DB> message: "surf_WIN32.exe has caused an error and will be closed.
> DB> Restart the program". I have about 10 GB free space on the H:\temp.
> DB> Win2k, AMD 1800, 512 MB RAM. Is this not sufficient? How could I
> DB> proceed?
> DB> Thanx for hints, Dieter
>
>
> dieter,
>
> well, i don't know the exact limits of the surf program,
> but for calculating and displaying the surface, you should
> not need the 'internal' atoms.
> so i would try to use the surface visualization only
> on a selection of 'outside' atoms.
>
> e.g. by identifying an atom in the center and then
> using a selection like 'not within xx.x of index yy'
> for the surface visualization. at that scale perhaps
> also a VDW visualization with a slightly increased
> radius could work well enough.
>
> axel.
>
> DB> On 28 Dec 2004 at 15:37, Axel Kohlmeyer wrote:
>
> >> On Tue, 28 Dec 2004, dieter blaas wrote:
> >>
> >> dieter,
> >>
> DB> I have been trying hard to render the surface of a virus-receptor
> DB> complex (1v9u.pdb) but always get the message "ERROR) Failed to
> DB> create Surf atom radii input file". Since I believed that this is related to
> >>
> >> this message more likely indicates, that you have not set the
> >> VMDTMPDIR environment variable or it points to a non-writable
> >> or non-existing directory. the fact, that it also happens with
> >> a smaller file confirms that.
> >>
> >> please check the VMD installation instructions.
> >> for more specific suggestions, we'd need to
> >> know which platform/OS you are using (and which VMD version).
> >>
> >> regards,
> >> axel.
> >>
> DB> the large coordinate file I also tried to render a surface of a small
> DB> molecule. However, in all cases I receive the same message. What is
> DB> the reason?
> DB> Thanx for help, Dieter
> DB>
> DB>
> >>
> >> --
> >>
> >> =======================================================================
> >> Dr. Axel Kohlmeyer e-mail: axel.kohlmeyer_at_theochem.ruhr-uni-bochum.de
> >> Lehrstuhl fuer Theoretische Chemie Phone: ++49 (0)234/32-26673
> >> Ruhr-Universitaet Bochum - NC 03/53 Fax: ++49 (0)234/32-14045
> >> D-44780 Bochum http://www.theochem.ruhr-uni-bochum.de/~axel.kohlmeyer/
> >> =======================================================================
> >> If you make something idiot-proof, the universe creates a better idiot.
> >>
>
>
>
>
> --
>
> =======================================================================
> Axel Kohlmeyer e-mail: axel.kohlmeyer_at_theochem.ruhr-uni-bochum.de
> Lehrstuhl fuer Theoretische Chemie Phone: ++49 (0)234/32-26673
> Ruhr-Universitaet Bochum - NC 03/53 Fax: ++49 (0)234/32-14045
> D-44780 Bochum http://www.theochem.ruhr-uni-bochum.de/~axel.kohlmeyer/
> =======================================================================
> If you make something idiot-proof, the universe creates a better idiot. 

-- 
NIH Resource for Macromolecular Modeling and Bioinformatics
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