Protein Database Downloader - Grasshopper2024-03-29T10:52:23Zhttps://www.grasshopper3d.com/forum/topics/protein-database-downloader?commentId=2985220%3AComment%3A1784693&x=1&feed=yes&xn_auth=noImpressed to learn ribbons ar…tag:www.grasshopper3d.com,2016-05-03:2985220:Comment:15212122016-05-03T03:28:07.046ZNik Willmorehttps://www.grasshopper3d.com/profile/NikFromNYC
<p>Impressed to learn ribbons are not just contained in the PDB file but require geometry testing of angles of the bond network.</p>
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<p>I'm not getting great results yet though with either lysenin pore 5GAQ or the big ring 3J1W. Lysenin shows only one of the nine segments, oddly too since it seems to output more but on baking I don't see duplicates, maybe just a single duplicate ribbon collection. 3J1W gives a single unit too, but very oddly it is entirely flattened into the XZ…</p>
<p>Impressed to learn ribbons are not just contained in the PDB file but require geometry testing of angles of the bond network.</p>
<p></p>
<p>I'm not getting great results yet though with either lysenin pore 5GAQ or the big ring 3J1W. Lysenin shows only one of the nine segments, oddly too since it seems to output more but on baking I don't see duplicates, maybe just a single duplicate ribbon collection. 3J1W gives a single unit too, but very oddly it is entirely flattened into the XZ plane.</p>
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<p>These both take about 6 minutes to process, sorry, but symmetry does add up.</p>
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<p>I've enclosed just my Python reader and the big ring, which proves the file itself contains all the units.</p>
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<p>This is a different issue than my original lamentation that some PDB files lack the whole virus or whole cylindrical assembly, and I wondered how they 3D plotted the whole thing, where they got the symmetry information from.</p> Hi Nick,
Thanks for catching…tag:www.grasshopper3d.com,2016-05-02:2985220:Comment:15209462016-05-02T22:18:33.311ZRyan Hooverhttps://www.grasshopper3d.com/profile/0knpc7lo01jbv
<p>Hi Nick,</p>
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<p>Thanks for catching these errors. The protein tools and one other simply dd not make it into the build somehow. This has been fixed and you can download the full package now.</p>
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<p>Thanks for pointing out the issue with gHowl too. I had forgotten that I was using the gHowl XML parser in the PDB Query tool. I decided to simplify that for the user and wrote my own version. It is more specific to the RCSB query reply, which may make it a little more robust. The…</p>
<p>Hi Nick,</p>
<p></p>
<p>Thanks for catching these errors. The protein tools and one other simply dd not make it into the build somehow. This has been fixed and you can download the full package now.</p>
<p></p>
<p>Thanks for pointing out the issue with gHowl too. I had forgotten that I was using the gHowl XML parser in the PDB Query tool. I decided to simplify that for the user and wrote my own version. It is more specific to the RCSB query reply, which may make it a little more robust. The nice thing about these changes is that I was able to get it the full query cycle to run about 20x faster. While I was in there working on the protein tools, I made a few other upgrades. The PDB Open tool will now take a PDB ID as an input and and download it from RCSB. The Protein Ribbon visualizer now allows you to move and orient the protein. There were a few other tweaks that would only make sense to point out if you had already been working with these tools.</p>
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<p>I appreciate your feedback thus far. I look forward to hearing more once you have the full package.</p>
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<p>Cheers,</p>
<p>rh</p> New problem: the Protein tab…tag:www.grasshopper3d.com,2016-05-02:2985220:Comment:15201092016-05-02T03:52:53.892ZNik Willmorehttps://www.grasshopper3d.com/profile/NikFromNYC
<p>New problem: the Protein tab is missing that I see here in your screenshot, but the rest is intact.</p>
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<p><a href="http://www.ryanhoover.org/images/Alba_Demo_GFP_DNA_TxTl_ProteinQuery_Viz_wToolbar.png" rel="nofollow" target="_blank">http://www.ryanhoover.org/images/Alba_Demo_GFP_DNA_TxTl_ProteinQuer...</a></p>
<p><a href="http://storage.ning.com/topology/rest/1.0/file/get/2769144448?profile=original" target="_self"><img class="align-full" src="http://storage.ning.com/topology/rest/1.0/file/get/2769144448?profile=RESIZE_1024x1024" width="721"></img></a></p>
<p>Tried with both latest Rhino/Grasshopper and…</p>
<p>New problem: the Protein tab is missing that I see here in your screenshot, but the rest is intact.</p>
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<p><a rel="nofollow" href="http://www.ryanhoover.org/images/Alba_Demo_GFP_DNA_TxTl_ProteinQuery_Viz_wToolbar.png" target="_blank">http://www.ryanhoover.org/images/Alba_Demo_GFP_DNA_TxTl_ProteinQuer...</a></p>
<p><a href="http://storage.ning.com/topology/rest/1.0/file/get/2769144448?profile=original" target="_self"><img width="721" src="http://storage.ning.com/topology/rest/1.0/file/get/2769144448?profile=RESIZE_1024x1024" width="721" class="align-full"/></a></p>
<p>Tried with both latest Rhino/Grasshopper and Rhino 6 WIP. No files were blocked in Windows. Using 64 bit Windows 7. Tried placing folder in User Objects as well as individual folder contents. There are 43 files, which is indeed 4 files short of how many components you show.</p>
<p><a href="http://storage.ning.com/topology/rest/1.0/file/get/2769144800?profile=original" target="_self"><img src="http://storage.ning.com/topology/rest/1.0/file/get/2769144800?profile=original" width="635" class="align-full"/></a></p>
<p>I noticed one sample file also required gHowl and also installed that.</p>
<p></p> Thanks for letting me know, N…tag:www.grasshopper3d.com,2016-05-01:2985220:Comment:15203412016-05-01T23:36:27.364ZRyan Hooverhttps://www.grasshopper3d.com/profile/0knpc7lo01jbv
<p>Thanks for letting me know, Nick. It is fixed now.</p>
<p>Thanks for letting me know, Nick. It is fixed now.</p> Lysenin pore:
http://www.rcs…tag:www.grasshopper3d.com,2016-04-30:2985220:Comment:15194162016-04-30T05:26:12.497ZNik Willmorehttps://www.grasshopper3d.com/profile/NikFromNYC
<p>Lysenin pore:</p>
<p><a href="http://storage.ning.com/topology/rest/1.0/file/get/2769142586?profile=original" target="_self"><img class="align-full" src="http://storage.ning.com/topology/rest/1.0/file/get/2769142586?profile=original" width="720"></img></a></p>
<p><a href="http://www.rcsb.org/pdb/explore/explore.do?structureId=5gaq" rel="nofollow" target="_blank">http://www.rcsb.org/pdb/explore/explore.do?structureId=5gaq</a></p>
<p><iframe allowfullscreen="" frameborder="0" height="267" src="https://www.youtube.com/embed/utKVyf9e2tw?wmode=opaque" width="475"></iframe>
</p>
<p>Part of a worm toxin. Creates…</p>
<p>Lysenin pore:</p>
<p><a href="http://storage.ning.com/topology/rest/1.0/file/get/2769142586?profile=original" target="_self"><img src="http://storage.ning.com/topology/rest/1.0/file/get/2769142586?profile=original" width="720" class="align-full"/></a></p>
<p><a rel="nofollow" href="http://www.rcsb.org/pdb/explore/explore.do?structureId=5gaq" target="_blank">http://www.rcsb.org/pdb/explore/explore.do?structureId=5gaq</a></p>
<p><iframe width="475" height="267" src="https://www.youtube.com/embed/utKVyf9e2tw?wmode=opaque" frameborder="0" allowfullscreen=""></iframe>
</p>
<p>Part of a worm toxin. Creates holes in cell membranes.</p> Ryan, your download link is f…tag:www.grasshopper3d.com,2016-04-30:2985220:Comment:15192192016-04-30T01:11:03.096ZNik Willmorehttps://www.grasshopper3d.com/profile/NikFromNYC
<p>Ryan, your download link is failing for both your plug-ins:</p>
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<p>"<span>Error: INSERT INTO users (first, last, email, field, comment, date, timestamp) VALUES ('Nik', 'Willmore', 'nikwillmore@gmail.com', '', '','2016-04-29 20:39:48 Friday','1461976788' )"</span></p>
<p>Ryan, your download link is failing for both your plug-ins:</p>
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<p>"<span>Error: INSERT INTO users (first, last, email, field, comment, date, timestamp) VALUES ('Nik', 'Willmore', 'nikwillmore@gmail.com', '', '','2016-04-29 20:39:48 Friday','1461976788' )"</span></p> Today's highlight was a hea…tag:www.grasshopper3d.com,2016-04-20:2985220:Comment:15122002016-04-20T16:48:12.890ZNik Willmorehttps://www.grasshopper3d.com/profile/NikFromNYC
<p><a href="http://storage.ning.com/topology/rest/1.0/file/get/2769140581?profile=original" target="_self"><img class="align-full" src="http://storage.ning.com/topology/rest/1.0/file/get/2769140581?profile=original" width="640"></img></a></p>
<p><a href="http://storage.ning.com/topology/rest/1.0/file/get/2769140917?profile=original" target="_self"><img class="align-full" src="http://storage.ning.com/topology/rest/1.0/file/get/2769140917?profile=original" width="610"></img></a></p>
<p>Today's highlight was a heat shock protein cluster, for instance, but loading it into iMolview only gives one unit:…</p>
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<p><a href="http://storage.ning.com/topology/rest/1.0/file/get/2769140581?profile=original" target="_self"><img src="http://storage.ning.com/topology/rest/1.0/file/get/2769140581?profile=original" width="640" class="align-full"/></a></p>
<p><a href="http://storage.ning.com/topology/rest/1.0/file/get/2769140917?profile=original" target="_self"><img src="http://storage.ning.com/topology/rest/1.0/file/get/2769140917?profile=original" width="610" class="align-full"/></a></p>
<p>Today's highlight was a heat shock protein cluster, for instance, but loading it into iMolview only gives one unit:</p>
<p></p>
<p><span><a href="https://twitter.com/PDBeurope/status/722671886333841409" target="_blank">https://twitter.com/PDBeurope/status/722671886333841409</a></span></p>
<p></p> ...also, PDB models often lac…tag:www.grasshopper3d.com,2016-04-20:2985220:Comment:15123412016-04-20T15:05:01.088ZNik Willmorehttps://www.grasshopper3d.com/profile/NikFromNYC
<p><span>...also, PDB models often lack the full often radially symmetrical assembly, only giving one unit, and I don't know how to recreate the full protein machine like the PDB page often indeed shows fully assembled.</span></p>
<p><span>...also, PDB models often lack the full often radially symmetrical assembly, only giving one unit, and I don't know how to recreate the full protein machine like the PDB page often indeed shows fully assembled.</span></p> Ribbons! Fun candy.
I'd also…tag:www.grasshopper3d.com,2016-04-20:2985220:Comment:15121722016-04-20T14:43:18.152ZNik Willmorehttps://www.grasshopper3d.com/profile/NikFromNYC
<p>Ribbons! Fun candy.</p>
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<p>I'd also like to surface electron microscope surface files, not just solved molecule ones:</p>
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<p><a href="http://www.emdatabank.org/">http://www.emdatabank.org/</a></p>
<p>Ribbons! Fun candy.</p>
<p></p>
<p>I'd also like to surface electron microscope surface files, not just solved molecule ones:</p>
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<p><a href="http://www.emdatabank.org/">http://www.emdatabank.org/</a></p> This looks great, Nick. Thank…tag:www.grasshopper3d.com,2016-04-18:2985220:Comment:15110302016-04-18T18:17:20.510ZRyan Hooverhttps://www.grasshopper3d.com/profile/0knpc7lo01jbv
<p>This looks great, Nick. Thanks for sharing. You may also be interested in the suite of Grasshopper tools called "Alba" that I've just release for synthetic biology. It i</p>
<p>ncludes a component that allows you to search an amino acid sequence on RCSB, download the best match, and visualize the structure of the protein as a "ribbon" showing beta sheets and alpha helices. You can find more info and download it <a href="http://www.ryanhoover.org/rd/alba.php" target="_blank">h…</a></p>
<p>This looks great, Nick. Thanks for sharing. You may also be interested in the suite of Grasshopper tools called "Alba" that I've just release for synthetic biology. It i</p>
<p>ncludes a component that allows you to search an amino acid sequence on RCSB, download the best match, and visualize the structure of the protein as a "ribbon" showing beta sheets and alpha helices. You can find more info and download it <a href="http://www.ryanhoover.org/rd/alba.php" target="_blank">h</a><a href="http://www.ryanhoover.org/rd/alba.php" target="_blank">ere</a>. </p>
<p></p>
<p>Cheers,</p>
<p>Ryan</p>
<p><img src="http://www.ryanhoover.org/images/Alba_Demo_GFP_DNA_TxTl_ProteinQuery_Viz_expression.png?width=300" width="300" class="align-left"/><a href="http://www.ryanhoover.org/images/GFP_Protein_viz_1.png" target="_blank"><img src="http://www.ryanhoover.org/images/GFP_Protein_viz_1.png?width=300" width="300" class="align-full"/></a></p>