Hi Bob - I've tried exporting several different types of models to .wrl in both
RGB and CMYK color spaces, and haven't seen any colors output with negative
values. For example, this works fine for me:
fab AAA, polyala
python
for rep in ["lines", "spheres", "sticks", "surface", "cartoon"]:
cmd.show_as(rep)
cmd.save("rgb_%s.wrl" % rep)
cmd.space("cmyk")
cmd.save("cmyk_%s.wrl" % rep)
python end
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 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 .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 Frog [gratefulf...@gmail.com]
Sent: Saturday, May 03, 2014 1:53 PM
To: Sampson, Jared
Cc: Marcelo Marcet; pymol-users@lists.sourceforge.net
Subject: Re: [PyMOL] Pymol wrl output
Hi,
I tried it in white WRL as you suggested and that loaded into Shapeways ok.
Green would also load...
The same file, then set to CMYK colors (menu DISPLAY / COLOR SPACE / CMYK )
would not load...
Any help would be great!
Thanks for all this!
Ciao,
Bob
On Sat, May 3, 2014 at 6:44 PM, Sampson, Jared
<jared.samp...@nyumc.org<mailto:jared.samp...@nyumc.org>> wrote:
Hi Bob -
The reason you're getting these errors is because having negative values in a
color tuple is not meaningful (you can't have a negative amount 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 white` on
the command line) and see what that does.
Cheers,
Jared
--
Jared Sampson
Xiangpeng Kong Lab
NYU School of Medicine
kong.med.nyu.edu<http://kong.med.nyu.edu>
________________________________
From: Grateful Frog [gratefulf...@gmail.com<mailto:gratefulf...@gmail.com>]
Sent: Friday, May 02, 2014 7:07 PM
To: Marcelo Marcet
Cc: pymol-users@lists.sourceforge.net<mailto: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 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 shells.
Please visit your 3D model page to update your
file:http://www.shapeways.com/model/upload-and-buy/1932482<http://www.shapeways.com/model/upload-and-buy/1932482?etId=14290783&utm_source=automated-contact&utm_medium=email&utm_campaign=model-processing-failed>
Our tutorials and
FAQ<http://www.shapeways.com/support?etId=14290783&utm_source=automated-contact&utm_medium=email&utm_campaign=model-processing-failed>
can be super helpful for more detailed information, or you can always ask the
community a specific question on our
forum<http://www.shapeways.com/forum?etId=14290783&utm_source=automated-contact&utm_medium=email&utm_campaign=model-processing-failed>
If you're stuck or have any questions, don't hesitate to reach out at
serv...@shapeways.com<mailto:serv...@shapeways.com>. Please include the file as
an attachment to the email, as well as any notes on your design, so we can help
you solve your problem as quickly as possible.
Additional non-critical errors:
* Invalid field, unparsable value, name: Material.diffuseColor , value:
[-1.0, -1.0, 1.0]. Value ignored.
* Invalid field, unparsable value, name: Material.diffuseColor , value:
[-1.0, -1.0, 1.0]. Value ignored.
* Invalid field, unparsable value, name: Material.diffuseColor , value:
[-1.0, -1.0, 1.0]. Value ignored.
-> this goes on for tons of lines...
On Sat, May 3, 2014 at 12:39 AM, Grateful Frog
<gratefulf...@gmail.com<mailto:gratefulf...@gmail.com>> wrote:
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 Sat, May 3, 2014 at 12:17 AM, Marcelo Marcet
<mmar...@nait.ca<mailto:mmar...@nait.ca>> wrote:
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
<gratefulf...@gmail.com<mailto:gratefulf...@gmail.com>> wrote:
> 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 write the file to disk.
>
> This file can be visualized fine in MeshLab.
>
> However, it cannot be 3D printed at Shapeways. The error message does not say
> what is wrong.
>
> The work-around that I have found is to open the wrl file, generated by
> Pymol, in Meshlab and re-save another copy as wrl, but generated by Meshlab.
> This new file can be 3D printed at Shapeways.
>
> However, the look of the surface is not as nice when it comes out of Meshlab,
> as it is in Pymol...
>
> Any thoughts would be great!
>
> Thanks,
> Bob
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