HI David,
Thanks for that tip. I didn't understand where the menu show > as >
surface is?
But, I did "Hide everything", then "Show Suface" and Shapeways liked it!
So I now have a working solution!
Thanks EVERYONE!
This is a great support mailing list!
Ciao,
Bob
On Sun, May 4, 2014 at 2:08 PM, David Hall <li...@cowsandmilk.net> wrote:
> 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
>>>>>> >
>>>>>> ------------------------------------------------------------------------------
>>>>>> > "Accelerate Dev Cycles with Automated Cross-Browser Testing - For
>>>>>> FREE
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>>>>>>
>>>>>>
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