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Re: [PyMOL] Pymol wrl output
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From: David H. <li...@co...> - 2014-05-04 12:09:02
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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 <gra...@gm...>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 <Jar...@ny...>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 [gra...@gm...] >> *Sent:* Saturday, May 03, 2014 1:53 PM >> *To:* Sampson, Jared >> *Cc:* Marcelo Marcet; pym...@li... >> >> *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 <Jar...@ny...>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 [gra...@gm...] >>> *Sent:* Friday, May 02, 2014 7:07 PM >>> *To:* Marcelo Marcet >>> *Cc:* pym...@li... >>> *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 >>> se...@sh.... 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 <gra...@gm...>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 <MM...@na...>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 <gra...@gm...> >>>>> 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 >>>>> > Instantly run your Selenium tests across 300+ browser/OS combos. Get >>>>> > unparalleled scalability from the best Selenium testing platform >>>>> available. >>>>> > Simple to use. Nothing to install. 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