Have you tried doing show > as > surface
It appears the wrl file has a bunch of extra information from the cartoon
representation, which could confuse shapeways?
-David
On Sun, May 4, 2014 at 4:49 AM, Grateful Frog <gratefulf...@gmail.com>wrote:
> Hi Jared & everyone,
>
> First, thanks for all your help. I really appreciate it and am sorry to be
> such a noobie here...
>
> I am using the Pymol GUI (1.7).
>
> I've created a shared
> folder<https://drive.google.com/folderview?id=0B122hIUVdAXaWHN1X3dkS2VrQ1k&usp=sharing>with
> all my files so you can test with them if you like.
>
> The important files are:
>
> - TMD11.pdb : the source model
> - *TMD11Ultracmyk.wrl.zip* : the output file from Pymol which fails to
> 3D print at Shapeways. *THIS IS THE FILE THAT I WANT TO PRINT!*
> - TMD11UltracmykMesh.wrl.zip : the wrl output from MeshLab starting
> from the wrl from Pymol, which does print at Shapeways.
>
> My process is:
>
> 1. File / Open TMD11.pdb
> 2. show surface
> 3. Display / Quality / Maximum Quality
> 4. Display / Color Space / CMYK (For Publications)
> 5. File / Save Image As / VRML 2
> 6. end
>
> I do not know what is wrong with this file since Shapeways does not
> provide any useful error message.
>
> If I save the model as a single color wrl file, it can print fine.
>
> Thanks again for any help!
>
> Ciao, Bob.
>
>
>
>
>
> On Sun, May 4, 2014 at 1:29 AM, Sampson, Jared <jared.samp...@nyumc.org>wrote:
>
>> 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>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
>>> ------------------------------
>>> *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
>>>
>>> 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. 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>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>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>
>>>>> 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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