VMD-L Mailing List

From: Kevin C Chan (cchan2242-c_at_my.cityu.edu.hk)
Date: Wed Oct 15 2014 - 08:39:39 CDT

Thanks Stone, it looks much better now. Do you also have suggestions for the materials of the protein inside the transparent surfaces? Now I am using Diffuse and AOs as suggested on the webpage.

Also I could not quite get how the two light coefficient works, what is the difference among them and your glowlight.tcl (appeared in the mailing list) if what I want is light up the protein inside the surfaces only.

Cheers,

Kevin
ukevi_at_gmx.hk
On 13 Oct, 2014, at 21:59, John Stone <johns_at_ks.uiuc.edu> wrote:

> Hi,
> I would suggest that you try using the "GlassBubble" material for
> your transparent surface. It should case only very weak shadows, but
> it will hopefully clearly show the interesting boundaries of the
> outer molecular surfaces without obscuring interior cartoon representations.
> Give that a try and tell us what you think...
>
> Cheers,
> John Stone
> vmd_at_ks.uiuc.edu
>
> On Mon, Oct 13, 2014 at 09:48:21PM +0800, Kevin C Chan wrote:
>> It gives shadows from the curved surface which confuses with the cartoon
>> representations underneath.
>> Kevin
>> [1]ukevi_at_gmx.hk
>> On 13 Oct, 2014, at 14:52, Norman Geist
>> <[2]norman.geist_at_uni-greifswald.de> wrote:
>>
>> What exactly does *less satisfactory* look like?
>>
>> Norman Geist.
>>
>> Von: [3]owner-vmd-l_at_ks.uiuc.edu [[4]mailto:owner-vmd-l_at_ks.uiuc.edu] Im
>> Auftrag von Kevin C Chan
>> Gesendet: Montag, 13. Oktober 2014 06:39
>> An: VMD Mailing List
>> Betreff: vmd-l: Transparency rendering by Tachyon
>>
>> Dear VMD users and Stone,
>>
>> I am currently encounter questions about Tachyon image rendering in VMD.
>> Refer
>> to [5]http://www.ks.uiuc.edu/Research/vmd/minitutorials/tachyonao/, I am
>> very pleased by turning on AO. However whenever a transparent surface is
>> present, it is less satisfactory. I have browsed the mailing-list and
>> tried options like trans_vmd but it does not help much.
>>
>> Can anyone share some experience on rendering images involving
>> transparency, for instance, a transparent surface of the protein outside
>> its cartoon representation?
>>
>> Thanks so much.
>>
>> Kevin
>> [6]ukevi_at_gmx.hk
>>
>> ---------------------------------------------------------------------------
>>
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>> References
>>
>> Visible links
>> 1. mailto:ukevi_at_gmx.hk
>> 2. mailto:norman.geist_at_uni-greifswald.de
>> 3. mailto:owner-vmd-l_at_ks.uiuc.edu
>> 4. mailto:owner-vmd-l_at_ks.uiuc.edu
>> 5. http://www.ks.uiuc.edu/Research/vmd/minitutorials/tachyonao/
>> 6. mailto:ukevi_at_gmx.hk
>> 7. http://www.avast.com/
>> 8. http://www.avast.com/
>
> --
> NIH Center for Macromolecular Modeling and Bioinformatics
> Beckman Institute for Advanced Science and Technology
> University of Illinois, 405 N. Mathews Ave, Urbana, IL 61801
> http://www.ks.uiuc.edu/~johns/ Phone: 217-244-3349
> http://www.ks.uiuc.edu/Research/vmd/