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#pymol

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Bose-Einstein-Kondensat<p><a href="https://mstdn.social/tags/OpenSource" class="mention hashtag" rel="tag">#<span>OpenSource</span></a> multicolor <a href="https://mstdn.social/tags/3Dprinted" class="mention hashtag" rel="tag">#<span>3Dprinted</span></a> <a href="https://mstdn.social/tags/molecular" class="mention hashtag" rel="tag">#<span>molecular</span></a> <a href="https://mstdn.social/tags/orbital" class="mention hashtag" rel="tag">#<span>orbital</span></a> models for a 1st semester organic <a href="https://mstdn.social/tags/chemistry" class="mention hashtag" rel="tag">#<span>chemistry</span></a> course:</p><p>- <a href="https://mstdn.social/tags/classroom" class="mention hashtag" rel="tag">#<span>classroom</span></a>-acessible MO theory<br />- transition state understanding<br />- <a href="https://mstdn.social/tags/PyMOL" class="mention hashtag" rel="tag">#<span>PyMOL</span></a>- / <a href="https://mstdn.social/tags/Blender" class="mention hashtag" rel="tag">#<span>Blender</span></a>-exported .stl files</p><p><a href="https://doi.org/10.1021/acs.jchemed.4c00945" target="_blank" rel="nofollow noopener noreferrer" translate="no"><span class="invisible">https://</span><span class="ellipsis">doi.org/10.1021/acs.jchemed.4c</span><span class="invisible">00945</span></a><br /><a href="https://mstdn.social/tags/DIYchem" class="mention hashtag" rel="tag">#<span>DIYchem</span></a> <a href="https://mstdn.social/tags/lab" class="mention hashtag" rel="tag">#<span>lab</span></a> <a href="https://mstdn.social/tags/tools" class="mention hashtag" rel="tag">#<span>tools</span></a> <a href="https://mstdn.social/tags/education" class="mention hashtag" rel="tag">#<span>education</span></a> <a href="https://mstdn.social/tags/CompChem" class="mention hashtag" rel="tag">#<span>CompChem</span></a> <a href="https://mstdn.social/tags/STEM" class="mention hashtag" rel="tag">#<span>STEM</span></a> <a href="https://mstdn.social/tags/Chemie" class="mention hashtag" rel="tag">#<span>Chemie</span></a> <a href="https://mstdn.social/tags/Schule" class="mention hashtag" rel="tag">#<span>Schule</span></a> <a href="https://mstdn.social/tags/MINT" class="mention hashtag" rel="tag">#<span>MINT</span></a></p>
Luis Falcon<p>Slide from my talk "Open Science for Medicine and Society" at Komazawa university. Using GNU Health to select a BRCA1 variant involved in breast <a href="https://todon.eu/tags/cancer" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#<span>cancer</span></a> and the 3D representation of the BRCT domain using PyMOL.<br>Having access to the latest scientific evidence makes a huge difference in patients, yet medical research is being dismantled by <a href="https://todon.eu/tags/corporatocracy" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#<span>corporatocracy</span></a>. <br>Medicine and society evolves not because of the bullshit hype of AI, but because of the effort and talent of the men and women behind these projects. Respect :anarchoheart3: 🩺 <br><a href="https://todon.eu/tags/UniProt" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#<span>UniProt</span></a> <a href="https://todon.eu/tags/HUGO" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#<span>HUGO</span></a> <a href="https://todon.eu/tags/GNUHealth" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#<span>GNUHealth</span></a> <a href="https://todon.eu/tags/PyMOL" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#<span>PyMOL</span></a> <a href="https://todon.eu/tags/NIH" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#<span>NIH</span></a> <a href="https://todon.eu/tags/genomics" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#<span>genomics</span></a> <a href="https://todon.eu/tags/OpenScience" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#<span>OpenScience</span></a></p>
Patrёshkё<p><a href="https://quietplace.xyz/tags/DNA" rel="nofollow noopener noreferrer" target="_blank">#DNA</a> <a href="https://quietplace.xyz/tags/pymol" rel="nofollow noopener noreferrer" target="_blank">#pymol</a></p>
Patrёshkё<p><a href="https://quietplace.xyz/tags/alanine" rel="nofollow noopener noreferrer" target="_blank">#alanine</a> <a href="https://quietplace.xyz/tags/pymol" rel="nofollow noopener noreferrer" target="_blank">#pymol</a> <a href="https://quietplace.xyz/tags/pdb" rel="nofollow noopener noreferrer" target="_blank">#pdb</a><span> <br></span>​:blobfoxaww:​</p>
ericmjl<p>Switching to my favorite class of topics -- technical tips and tricks! This time round, it's about controlling <a href="https://octodon.social/tags/PyMOL" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#<span>PyMOL</span></a>, but instead of writing a script and executing it within PyMOL, with a bit of <a href="https://octodon.social/tags/LLM" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#<span>LLM</span></a> help, I figured out how to control PyMOL from within <a href="https://octodon.social/tags/Jupyter" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#<span>Jupyter</span></a> to make beautiful renderings of <a href="https://octodon.social/tags/protein" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#<span>protein</span></a> <a href="https://octodon.social/tags/structures" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#<span>structures</span></a>! As a bonus, I also showed how to take those renderings and lay them out using <a href="https://octodon.social/tags/matplotlib" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#<span>matplotlib</span></a>. <a href="https://bit.ly/3WMhJPo" rel="nofollow noopener noreferrer" translate="no" target="_blank"><span class="invisible">https://</span><span class="">bit.ly/3WMhJPo</span><span class="invisible"></span></a></p>
Bene<p>Help! I need to make a pretty image from a protein. Being old-school, I would use <a href="https://scholar.social/tags/pymol" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#<span>pymol</span></a>. </p><p>However, is there new stuff out there that 200-year old me doesn't know? Preferably, its <a href="https://scholar.social/tags/opensource" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#<span>opensource</span></a> or, if not, the license doesn't come at the price of a kidney.</p><p><a href="https://scholar.social/tags/molecular_graphics" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#<span>molecular_graphics</span></a><br> <br><span class="h-card" translate="no"><a href="https://mastodon.social/@helenajambor" class="u-url mention" rel="nofollow noopener noreferrer" target="_blank">@<span>helenajambor</span></a></span></p>
Cowboy Cat Ranch<p>Haven't found a solution to the problem yet. You'd expect something so simple shouldn't be that difficult to find.</p><p>Is there a way for me to manually rotate these molecules and align them? </p><p>I can align them in PyMol, but the alignment is not done how I want it done. </p><p>When I open both, select A, rotate A into the desired position, then select B, and rotate B, A has changed orientation. </p><p>Anybody any suggestions for manual alignment of small molecules?</p><p><a href="https://mastodon.online/tags/PyMol" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#<span>PyMol</span></a> <a href="https://mastodon.online/tags/chemistry" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#<span>chemistry</span></a> <a href="https://mastodon.online/tags/smallmolecules" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#<span>smallmolecules</span></a> <a href="https://mastodon.online/tags/ligands" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#<span>ligands</span></a></p>
Andrew Plested<p><span class="h-card" translate="no"><a href="https://mastodon.online/@cowboycatranch" class="u-url mention" rel="nofollow noopener noreferrer" target="_blank">@<span>cowboycatranch</span></a></span> <span class="h-card" translate="no"><a href="https://mastodon.online/@SRDas" class="u-url mention" rel="nofollow noopener noreferrer" target="_blank">@<span>SRDas</span></a></span> </p><p>This is a guess, but could it be the difference between model space and camera space?</p><p><a href="https://www.pymolwiki.org/index.php/Model_Space_and_Camera_Space" rel="nofollow noopener noreferrer" translate="no" target="_blank"><span class="invisible">https://www.</span><span class="ellipsis">pymolwiki.org/index.php/Model_</span><span class="invisible">Space_and_Camera_Space</span></a></p><p><a href="https://mstdn.science/tags/pymol" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#<span>pymol</span></a> <a href="https://mstdn.science/tags/molecules" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#<span>molecules</span></a></p>
Cowboy Cat Ranch<p>Is there a way for me to manually rotate these molecules and align them? </p><p>I can align them in PyMol, but the alignment is not done how I want it done. </p><p>When I open both, select A, rotate A into the desired position, then select B, and rotate B, A has changed orientation. </p><p>Anybody any suggestions for manual alignment of small molecules?</p><p><a href="https://mastodon.online/tags/PyMol" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#<span>PyMol</span></a> <a href="https://mastodon.online/tags/chemistry" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#<span>chemistry</span></a> <a href="https://mastodon.online/tags/smallmolecules" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#<span>smallmolecules</span></a></p>
Vaclav Hanzl<p><a href="https://sigmoid.social/tags/folding" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#<span>folding</span></a> <a href="https://sigmoid.social/tags/proteins" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#<span>proteins</span></a> by <a href="https://sigmoid.social/tags/NeuralNetwork" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#<span>NeuralNetwork</span></a> just for fun 'cause I can :)</p><p>Hard to believe that complete set of life's stock parts fits on screen: 22 <a href="https://sigmoid.social/tags/AminoAcids" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#<span>AminoAcids</span></a> + 4 <a href="https://sigmoid.social/tags/RNA" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#<span>RNA</span></a> blocks. Anything else can be made of these, or by tools made of these, or by tools made by tools made by... Including you and your computer. I am staring at it in transcendental <a href="https://sigmoid.social/tags/amazement" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#<span>amazement</span></a>.</p><p><a href="https://sigmoid.social/tags/3D" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#<span>3D</span></a> makes <a href="https://sigmoid.social/tags/biochemistry" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#<span>biochemistry</span></a> fun. And <a href="https://sigmoid.social/tags/FreeCAD" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#<span>FreeCAD</span></a> now feels easy after <a href="https://sigmoid.social/tags/PyMOL" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#<span>PyMOL</span></a> if <a href="https://sigmoid.social/tags/anaglyph" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#<span>anaglyph</span></a> glasses need a tweak :)</p>
Folmer<p>The innophore teams CavitOmiX for your <a href="https://mastodon.social/tags/PyMol" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#<span>PyMol</span></a> cavities<br><a href="https://mastodon.social/tags/StructuralBiology" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#<span>StructuralBiology</span></a><br><span class="h-card"><a href="https://a.gup.pe/u/structbio" class="u-url mention" rel="nofollow noopener noreferrer" target="_blank">@<span>structbio</span></a></span> <br><a href="https://mastodon.social/tags/proteinstructureandfunction" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#<span>proteinstructureandfunction</span></a> <br><a href="https://mastodon.social/tags/enzymeengineering" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#<span>enzymeengineering</span></a> </p><p><a href="https://pymolwiki.org/index.php/CavitOmiX" rel="nofollow noopener noreferrer" target="_blank"><span class="invisible">https://</span><span class="ellipsis">pymolwiki.org/index.php/CavitO</span><span class="invisible">miX</span></a></p>
Rike Mueller-Werkmeister<p><span class="h-card"><a href="https://fediscience.org/@MirandaLynchPhD" class="u-url mention" rel="nofollow noopener noreferrer" target="_blank">@<span>MirandaLynchPhD</span></a></span> haha 😂I think you bring huge amounts of knowledge- no need for that course;) - it’s really to interest a few master students (German system, not yet signed up for grad school) from chemistry for biophysics and structure (we really started out from protein structure fundamentals… but I also introduced the <a href="https://fediscience.org/tags/pdb" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#<span>pdb</span></a> <a href="https://fediscience.org/tags/pymol" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#<span>pymol</span></a> <a href="https://fediscience.org/tags/chimeraX" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#<span>chimeraX</span></a> in the first lecture, to make them explore protein structures along the way…</p>
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