VMD-L Mailing List

From: Peter Freddolino (petefred_at_ks.uiuc.edu)
Date: Tue Oct 21 2008 - 10:57:44 CDT

To add to Anton's comments, you may also want to experiment with
different renderers, which frequently treat transparency slightly
differently.
Best,
Peter

Anton Arkhipov wrote:
> 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 -----
>>
>>
>