VMD-L Mailing List

From: Axel Kohlmeyer (axel.kohlmeyer_at_theochem.ruhr-uni-bochum.de)
Date: Tue Dec 28 2004 - 10:14:27 CST

>>> "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.