Re: [PyMOL] exporting surfaces

2004-11-03 Thread D. Joe Anderson
On Wed, Oct 20, 2004 at 09:15:55AM -0600, C Want wrote:
 
 I wrote a cheap hack a while back to produce STL output for the 
 Connolly surfaces in pymol to help send some models to a 3D printer.
 Please see these previous messages for a 'patch' and some pictures:
 
 http://sourceforge.net/mailarchive/message.php?msg_id=5856368
 http://sourceforge.net/mailarchive/message.php?msg_id=5933822
 
 We have some 3D printer users in our Biochemistry department that
 still use this hack to get their models out of pymol.

Speaking of which, thanks again for that code, Chris.  I finally
got around to patching and compiling pymol, printing out a few
files, and tracking down a Zcorp 3D printer on campus here.  The
nice people who run it worked with me to print out a few parts
as they refer to them.  I printed 4 different PDB files, one I
use in my demos in class, and one each from three structural
biology groups in the department.

The structure I use in class is a complex made up of two chains. 
I was gratified to see that when printed as separate chains, the
two parts can be physically docked against one another pretty
well.  I had hoped that would be the case, but it's an entirely
different matter to hold the two pieces in one's hands and to
actually try to get them to fit!

The print outs have been well received so far (I've had them for
little over a week now) and we'll see if it gets enough interest
for us to make more such models.

One thing I did run into was trying to find a way of viewing the
generated .stl files.  In my searching, I thought I might be
able to use a combination of GTS (http://gts.sourceforge.net)
and GeomView (http://packages.debian.org/geomview) to do this,
but when I tried to take the stl files through the first stage
of the conversion, I got an error about the input not being a
valid stl file.  I'm hoping to get my hands on an stl file from
another source (AutoCAD, maybe?) and seeing if I can tease out
what the problem is.

-- 
D. Joe Anderson, Asst. Sci.2252 Molecular Biology Bldg. 
BBMB Research Computing Support
www.bb.iastate.edu/computing   bbsupp...@iastate.edu 



Re: [PyMOL] exporting surfaces

2004-10-20 Thread C Want

Subject: [PyMOL] exporting surfaces

Dear Pymol users,

Does anyone know if there is a way to export surfaces into a file format
suitable for import into 3D modellers (ie. Blender, 3DSMax, Lightwave, etc)?
For that matter, is it possible at all to export anything in pymol?


Hi Peter,

I wrote a cheap hack a while back to produce STL output for the 
Connolly surfaces in pymol to help send some models to a 3D printer.

Please see these previous messages for a 'patch' and some pictures:

http://sourceforge.net/mailarchive/message.php?msg_id=5856368
http://sourceforge.net/mailarchive/message.php?msg_id=5933822

We have some 3D printer users in our Biochemistry department that
still use this hack to get their models out of pymol.

I am also a blender developer (I'm supposed to work on the animation
tools, but I also occasionally add features to help with my work).
I added native STL import/export to blender a few versions ago... so
this might be one way to get your models into blender. The only problem
with this is that the STL format does not have support for colors,
so this is only a good solution if you are solely interested in
the shape of your surfaces. I think my 'patch' could easily be 
modified a bit to create a user-crufted file format for exporting the
colors with the geometry, and then python scripting in blender 
could be used to read this format (as Scott alluded to). This is the 
approach I use to get models out of VTK and into blender.


Regards,
Chris

Chris Want
Research Computing Support
Computing  Network Services
University of Alberta
Tel: 1-780-492-9418