• ## Outreach

From: John Stone (johns_at_ks.uiuc.edu)
Date: Tue Sep 06 2005 - 11:15:01 CDT

Kevin,
Glad you got this working. I'm CCing your note to VMD-L, there may
be some VMD users that want to make colored solid models of their molecules.
I know there are several of them down under :)

John Stone
vmd_at_ks.uiuc.edu

On Tue, Sep 06, 2005 at 12:06:33PM -0400, Kevin Smith wrote:
> Hi John,
> Thanks for your prompt response and help. Yes' it worked by toggle option. Even thou I couldn't make clean vrml but STL was spot on. It may be because I'm using vrml-1. I realised VRML works fine if you load single pdb file. We use few stl softwares like catalyst, solidview etc.
> Recently we are making lot of colored molecule models using Z-corp colored printer. Please let me know if you or some of your associates need colored parts we can always give you discounted price. By the way we are based in Australia. Thanks once again for your help.
>
> Kind Regards,
> Kevin
> arptech.com.au
>
>
>
> Thanks for your help again.
>
> Regards,
> Rick
>
> John Stone <johns_at_ks.uiuc.edu> wrote:
>
> >
> >Hi,
> > One way to solve the scale factor is to load all of the
> >PDB files into VMD at once. Once loaded, you can toggle all of
> >them off but one, render to STL, and repeat for each of the PDBs
> >you have loaded. You can automate this by script. That should cure
> >the scaling factor problem you're having.
> >Are you having the display problems only with VRML, or with both VRML
> >and STL? I don't know why your VRML/STL processing software won't d
> >isplay anything for the STL files produced by VMD, they work fine
> >with the software our 3-D printing lab uses here.
> >It could be that your software wants surface normals
> >and/or other information rather than just the triangulated surface?
> >What software are you loading the STL/VRML files into?
> >
> > John Stone
> > vmd_at_ks.uiuc.edu
> >
> >On Sat, Sep 03, 2005 at 02:56:27PM -0400, Kevin Smith wrote:
> >> Hi John,
> >> I got a bunch of PDB files which I'm trying to make vrml files for prototyping. All these molecules are interlocking to each other so all individual items should have same scaling factor.
> >> My problem is when I try to export MSMS to VRML individually, scale factor is changing and it seems to be there is no relation between them at all. I have also tried to load all pdb files but I can export only the first pdb file to vrml and remaining files have still large file size but can't display anything?
> >>
> >> Is there any scaling factor which will make sure the molecule size will be same everytime I export STL or VRML file?
> >>
> >> Thanks in advance.
> >>
> >> Kind Regards,
> >> Kevin
> >>
> >>
> >>
> >> John Stone <johns_at_ks.uiuc.edu> wrote:
> >>
> >> >Hi,
> >> > You'll want to use MSMS if you want to be able to control the
> >> >surface resolution. In order to use MSMS on the Windows version of
> >> >VMD, you need to install MSMS on your system somewhere. Once installed,
> >> >you'll then need to open "my computer" properties, go to the "advanced"
> >> >tab, open the "environment variables" window, and add a new "MSMSSERVER"
> >> >environment variable, which should be the fully qualified path to the
> >> >MSMS binary installed on your machine. (e.g. "c:\foo\bar\msms.exe" or
> >> >whatever...)
> >> >
> >> >Once you've done that, you should be able to use MSMS from within VMD,
> >> >and that will give you the best STL surface export.
> >> >
> >>
> >> > John Stone
> >> > vmd_at_ks.uiuc.edu
> >> >
> >> >On Wed, Aug 03, 2005 at 10:23:02AM -0400, Kevin Smith wrote:
> >> >> Hi All,
> >> >> I'm trying to convert PDB file to STL format for prototyping need using VMD 1.8.3 (windows). I can render VDW representation to STL without any trouble but I really need "surface" rep to be converted to STL. Problem I'm facing is; surface to STL resolution is very very coarse. In VDW rep I have control to increase the sphere resolution but nothing to change the resolution in "surface" draw mode. Could someone suggest how to make a smoother resolution STL file. I'm not worried about if any STL facets are missing or self intersecting because I can easily fix them with stl editor later on but I can't increase the file resolution.
> >> >> By the way I have also tried MSMS draw method but noting appears in graphic window. Any help would be highly appreciated. Thanks in advance.
> >> >>
> >> >> Regards,
> >> >> Kevin
> >> >>
> >> >>
> >> >> __________________________________________________________________
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> >--
> >NIH Resource for Macromolecular Modeling and Bioinformatics
> >Beckman Institute for Advanced Science and Technology
> >University of Illinois, 405 N. Mathews Ave, Urbana, IL 61801
> >Email: johns_at_ks.uiuc.edu Phone: 217-244-3349
> > WWW: http://www.ks.uiuc.edu/~johns/ Fax: 217-244-6078
> >
>
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--
NIH Resource for Macromolecular Modeling and Bioinformatics
Beckman Institute for Advanced Science and Technology
University of Illinois, 405 N. Mathews Ave, Urbana, IL 61801
Email: johns_at_ks.uiuc.edu                 Phone: 217-244-3349
WWW: http://www.ks.uiuc.edu/~johns/      Fax: 217-244-6078