if you're just typing the command, you can type "as surface" (or "show_as
surface") and it will only use the surface representation. The menu I'm
talking about is the letter [S] next to each object on the RHS of the
screen. The first line under Show: is as, which pops out another menu where
you can choose representations.
-David
On Sun, May 4, 2014 at 8:40 AM, Grateful Frog <gratefulf...@gmail.com>wrote:
> 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
>>>>>>> >
>>>>>>> ------------------------------------------------------------------------------
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