VMD-L Mailing List

From: Anton Arkhipov (anton_at_ks.uiuc.edu)
Date: Tue Oct 21 2008 - 10:43:40 CDT

Hi,

> 2. after rendering the resolution of the transparency is a mess and
> so i can not acquire a nice image

Have you tried changing "Isovalue" in the Graphical Representation of
your isosurface? You can also try varying "Step" in the
representation; a larger "Step" gives you are smoother map.

Another important thing you should consider is how you obtain the map.
To get a nice water box, I usually use the following settings in the
volmap plugin: selection = all; volmap type = density; resolution = 3
A; atom size = 3 A; weights = none. I'm sure there are other
combinations of these parameters that give a nice map too, but these
work for me... Also, what you get from volmap depends on what kind of
system you have - if it is dense or sparse, if it is just a water box
or it has some protein inside, etc.

Best,

Anton.

On 21 Oct 2008, at 09:07, Panagiota Georgoulia wrote:

> I have already tried that but there are two issues:
> 1. the image is not exactly the one i am trying to make (i think i
> should use glass/not tranparency)
> 2. after rendering the resolution of the transparency is a mess and
> so i can not acquire a nice image
>
>
> ----- Μήνυμα από petefred_at_ks.uiuc.edu ---------
> Ημερομηνία: Tue, 21 Oct 2008 07:26:23 -0500
> Από: Peter Freddolino <petefred_at_ks.uiuc.edu>
> Θέμα: Re: vmd-l: volmap
> Προς: Panagiota Georgoulia <pg9438_at_mbg.duth.gr>
> Κοινοποίηση: vmd-l_at_ks.uiuc.edu
>
>
>> You just need to load the .dx file into vmd, and then in the
>> graphical representations menu change the material to transparent,
>> Drawing method to isosurface, and Draw mode to Solid surface.
>> Best,
>> Peter
>>
>> Panagiota Georgoulia wrote:
>>> Could someone elaborate on how to use the volumetric map generated
>>> by the volmap plugin to make a transparent model of the solvent????
>>
>
>
> ----- End message from petefred_at_ks.uiuc.edu -----
>
>