Re: [PyMOL] Pymol wrl output

2014-05-06 Thread Hurt, Darrell (NIH/NIAID) [E]
From: David Hall mailto:li...@cowsandmilk.net>> Date: Sunday, May 4, 2014 8:48 AM To: Grateful Frog mailto:gratefulf...@gmail.com>> Cc: "pymol-users@lists.sourceforge.net<mailto:pymol-users@lists.sourceforge.net>" mailto:pymol-users@lists.sourceforge.net>> Sub

Re: [PyMOL] Pymol wrl output

2014-05-04 Thread David Hall
nd >>>> >>>> and it results in no instances of diffuseColor on the same line as a >>>> negative number in any of the output wrl files (as determined by: `grep >>>> -e "diffuseColor.*-" *.wrl` ). >>>> >>>> Could you be more spe

Re: [PyMOL] Pymol wrl output

2014-05-04 Thread Grateful Frog
: `grep >>> -e "diffuseColor.*-" *.wrl` ). >>> >>> Could you be more specific with how you're generating the colors in >>> your PyMOL session (perhaps with a minimal script that reproduces the >>> problem), and/or post a bit of the output

Re: [PyMOL] Pymol wrl output

2014-05-04 Thread David Hall
unt >>> of color), and results in undefined behavior. RGB colors use a number in >>> the range 0.0-1.0 (inclusive) for each value in the tuple. What color are >>> you using for your model before exporting VRML? Try setting everything to >>> white (`color wh

Re: [PyMOL] Pymol wrl output

2014-05-04 Thread Grateful Frog
or post a bit of the output .wrl file, showing in particular anywhere > you see a negative color value? > > Thanks, > Jared > > -- > Jared Sampson > Xiangpeng Kong Lab > NYU School of Medicine > kong.med.nyu.edu > -------------- > *From:* Grateful

Re: [PyMOL] Pymol wrl output

2014-05-03 Thread Sampson, Jared
g in particular anywhere you see a negative color value? Thanks, Jared -- Jared Sampson Xiangpeng Kong Lab NYU School of Medicine kong.med.nyu.edu From: Grateful Frog [gratefulf...@gmail.com] Sent: Saturday, May 03, 2014 1:53 PM To: Sampson, Jared Cc: Marcelo Marcet;

Re: [PyMOL] Pymol wrl output

2014-05-03 Thread Grateful Frog
ng Kong Lab > NYU School of Medicine > kong.med.nyu.edu > -- > *From:* Grateful Frog [gratefulf...@gmail.com] > *Sent:* Friday, May 02, 2014 7:07 PM > *To:* Marcelo Marcet > *Cc:* pymol-users@lists.sourceforge.net > *Subject:* Re: [PyMOL] Pymol wrl output &

Re: [PyMOL] Pymol wrl output

2014-05-03 Thread Sampson, Jared
teful Frog [gratefulf...@gmail.com] Sent: Friday, May 02, 2014 7:07 PM To: Marcelo Marcet Cc: pymol-users@lists.sourceforge.net Subject: Re: [PyMOL] Pymol wrl output these are the errors that Shapeways sent back: Unfortunately, the model you recently uploaded TMD11Ultra.wrl did not pass ou

Re: [PyMOL] Pymol wrl output

2014-05-02 Thread Grateful Frog
these are the errors that Shapeways sent back: Unfortunately, the model you recently uploaded TMD11Ultra.wrl did not pass our initial printability checks, so it's not yet ready for 3D printing. Printability Error: - Model failed during repair. This is likely due to problems merging shel

Re: [PyMOL] Pymol wrl output

2014-05-02 Thread Grateful Frog
Hi Marcelo, Thanks for your help and suggestion! I did that and the surface is much nicer. However, the Pymol rendering in VRML still won't load to Shapeways without error. I have to re-render in VRML in MeshLab. My goal is to do it all in Pymol. Any more ideas would be great! Ciao, Bob On

Re: [PyMOL] Pymol wrl output

2014-05-02 Thread Marcelo Marcet
Hi Bob, Before you save your file from pymol try increasing the quality to max, then save as VRML. This increases the number of polygons in the file and after exporting from meshlab the final molecule will look a lot smoother. Cheers, Marcelo On May 2, 2014, at 2:15 PM, Grateful Frog wrote:

[PyMOL] Pymol wrl output

2014-05-02 Thread Grateful Frog
Hi all, I'm new to this list and to this tool. I have encountered a problem with exporting as wrl in pylolk 1.7 that I compiled on my Ubuntu 12.04 platform. I load a PDB file and it displays fine. I then type the command "show surface" and this works fine, too. I then save image as VRML 2, and