Hi everyone, We are developing a new NIH web portal for freely preparing 3D print files from molecular, microscopy, and medical imaging data. The website is in public beta, so you may see some changes in the final release, but this email thread seemed like a good opportunity to make you aware of it. Anyone can browse and download files, but only registered users can create and upload 3D printable files to share.
If you have the PDB code, you can simply type it in (under "Create") and our tools will generate several different representations of the protein(s) that should be directly printable. Alternatively, if you have a custom PDB, you can simply upload it and get the same kind of output. Please give it a try and let us know what you think! http://3dprint.nih.gov Thanks, Darrell -- Darrell Hurt, Ph.D. Section Head, Computational Biology Bioinformatics and Computational Biosciences Branch (BCBB) OCICB/OSMO/OD/NIAID/NIH 31 Center Drive, Room 3B62B, MSC 2135 Bethesda, MD 20892-2135 Office: 301-402-0095 Mobile: 301-758-3559 Web: BCBB Home Page<http://www.niaid.nih.gov/about/organization/odoffices/omo/ocicb/Pages/bcbb.aspx#niaid_inlineNav_Anchor> Twitter: @niaidbioit<https://twitter.com/niaidbioit> Disclaimer: The information in this e-mail and any of its attachments is confidential and may contain sensitive information. It should not be used by anyone who is not the original intended recipient. If you have received this e-mail in error please inform the sender and delete it from your mailbox or any other storage devices. National Institute of Allergy and Infectious Diseases shall not accept liability for any statements made that are sender's own and not expressly made on behalf of the NIAID by one of its representatives. From: David Hall <li...@cowsandmilk.net<mailto:li...@cowsandmilk.net>> Date: Sunday, May 4, 2014 8:48 AM To: Grateful Frog <gratefulf...@gmail.com<mailto:gratefulf...@gmail.com>> Cc: "pymol-users@lists.sourceforge.net<mailto:pymol-users@lists.sourceforge.net>" <pymol-users@lists.sourceforge.net<mailto:pymol-users@lists.sourceforge.net>> Subject: Re: [PyMOL] Pymol wrl output 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<mailto: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<mailto: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<mailto: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<mailto: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<http://kong.med.nyu.edu> ________________________________ From: Grateful Frog [gratefulf...@gmail.com<mailto:gratefulf...@gmail.com>] Sent: Saturday, May 03, 2014 1:53 PM To: Sampson, Jared Cc: Marcelo Marcet; pymol-users@lists.sourceforge.net<mailto: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<mailto: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<http://kong.med.nyu.edu> ________________________________ From: Grateful Frog [gratefulf...@gmail.com<mailto:gratefulf...@gmail.com>] Sent: Friday, May 02, 2014 7:07 PM To: Marcelo Marcet Cc: pymol-users@lists.sourceforge.net<mailto: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<mailto: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<mailto: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<mailto: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<mailto: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 > 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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