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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>>>
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