Re: [PyMOL] exporting surfaces
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
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
[PyMOL] exporting surfaces
Hello Peter, This is something I've been struggling with for awhile now. You can export a povray file from PyMol (just search the list archives), but at the moment that's about it. I have written a small python plugin for Blender that can import the smooth_triangles from a PyMol/povray file. Of course this will only allow you to work with objects composed of triangles (surfaces), but if I had more time I think it wouldn't be too difficult to make the plugin work with other shapes too (i.e. spheres, cyclinders, etc.). If you would like my Blender plugin just let me know. Ciao, Scott On Oct 19, 2004, at 4:49 AM, Peter Dudek wrote: 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? I realize that asking for support of a particular 3D file format is a bit of a slippery slope - if one export format is supported, everyone will want support for their favourite format. This is why I embarked on a bit of a solitary crusade a few months ago - I wrote a small (and dubious) python script that converts MSMS calculated surfaces into the RAW file format, which *every* 3D modeller can import. Unfortunately, I could never figure out how to extrapolate or calculate the normals, so quite a bit of detail is lost in the conversion. How are surfaces calculated and stored in pymol? If writing an export filter/extension is trivial, I'd be willing to do it with a bit of hand holding. Cheers, Peter - Laboratory of Dr. Didier Picard University of Geneva Department of Cell Biology Sciences III 30, Quai Ernest-Ansermet 1211 Geneva 4 Switzerland Tel: +41 22 379 3254 Fax: +41 22 379 6442 Email: du...@cellbio.unige.ch http://www.picard.ch/DP/DPhome.html --- This SF.net email is sponsored by: IT Product Guide on ITManagersJournal Use IT products in your business? Tell us what you think of them. Give us Your Opinions, Get Free ThinkGeek Gift Certificates! Click to find out more http://productguide.itmanagersjournal.com/guidepromo.tmpl ___ PyMOL-users mailing list PyMOL-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/pymol-users Scott Classen, Ph.D. ACS Postdoctoral Fellow Department of Molecular & Cell Biology University of California, Berkeley 237 Hildebrand Hall #3206 Berkeley, CA 94720-3206 LAB 510.643.9491 FAX 510.643.9290
[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? I realize that asking for support of a particular 3D file format is a bit of a slippery slope - if one export format is supported, everyone will want support for their favourite format. This is why I embarked on a bit of a solitary crusade a few months ago - I wrote a small (and dubious) python script that converts MSMS calculated surfaces into the RAW file format, which *every* 3D modeller can import. Unfortunately, I could never figure out how to extrapolate or calculate the normals, so quite a bit of detail is lost in the conversion. How are surfaces calculated and stored in pymol? If writing an export filter/extension is trivial, I'd be willing to do it with a bit of hand holding. Cheers, Peter - Laboratory of Dr. Didier Picard University of Geneva Department of Cell Biology Sciences III 30, Quai Ernest-Ansermet 1211 Geneva 4 Switzerland Tel: +41 22 379 3254 Fax: +41 22 379 6442 Email: du...@cellbio.unige.ch http://www.picard.ch/DP/DPhome.html
