Today we remember Warren L. DeLano 21 June 1972–3 November 2009.
Creator and driving force behind Pymol www.nature.com/articles/nsm...
#ChemSky 🧪
Creator and driving force behind Pymol www.nature.com/articles/nsm...
#ChemSky 🧪
November 3, 2026 at 1:25 AM
Today we remember Warren L. DeLano 21 June 1972–3 November 2009.
Creator and driving force behind Pymol www.nature.com/articles/nsm...
#ChemSky 🧪
Creator and driving force behind Pymol www.nature.com/articles/nsm...
#ChemSky 🧪
ChimeraX is my tool of choice for viewing and interacting with cryo-EM maps and associated structural models. These files are typically huge & ChimeraX is much better at dealing with them than PyMOL is, though I still prefer PyMOL for most things.
youtu.be/XClXnxdwxVQ
youtu.be/XClXnxdwxVQ
Fetching and viewing cryo-EM maps & models in ChimeraX
YouTube video by the bumbling biochemist
youtu.be
October 31, 2026 at 7:42 PM
ChimeraX is my tool of choice for viewing and interacting with cryo-EM maps and associated structural models. These files are typically huge & ChimeraX is much better at dealing with them than PyMOL is, though I still prefer PyMOL for most things.
youtu.be/XClXnxdwxVQ
youtu.be/XClXnxdwxVQ
Authors published a paper in Biorxiv, they used PyMOL in the study. Including #RRIDs will make this less ambiguous.
SciScore made a table with this resource, see “Automated Services” module (download as csv, xml or #jats) #STMpublishing #reproducibility
SciScore made a table with this resource, see “Automated Services” module (download as csv, xml or #jats) #STMpublishing #reproducibility
www.biorxiv.org
November 3, 2026 at 1:00 PM
Authors published a paper in Biorxiv, they used PyMOL in the study. Including #RRIDs will make this less ambiguous.
SciScore made a table with this resource, see “Automated Services” module (download as csv, xml or #jats) #STMpublishing #reproducibility
SciScore made a table with this resource, see “Automated Services” module (download as csv, xml or #jats) #STMpublishing #reproducibility
Authors published a paper in Biorxiv, they used PyMOL in the study. Including #RRIDs will make this less ambiguous.
SciScore made a table with this resource, see “Automated Services” module (download as csv, xml or #jats) #STMpublishing #methodsmatter
SciScore made a table with this resource, see “Automated Services” module (download as csv, xml or #jats) #STMpublishing #methodsmatter
www.biorxiv.org
October 26, 2026 at 12:00 PM
Authors published a paper in Biorxiv, they used PyMOL in the study. Including #RRIDs will make this less ambiguous.
SciScore made a table with this resource, see “Automated Services” module (download as csv, xml or #jats) #STMpublishing #methodsmatter
SciScore made a table with this resource, see “Automated Services” module (download as csv, xml or #jats) #STMpublishing #methodsmatter
🧬 Meet PROTFIG! An open-source tool for automatically generating publication-quality biomolecular figures with PyMOL.
🔗 github.com/AmericaChi/P...
🔗https://biorxiv.org/content/10.64898/2026.10.20.760606v1
#StructuralBiology #PyMOL #OpenScience
🔗 github.com/AmericaChi/P...
🔗https://biorxiv.org/content/10.64898/2026.10.20.760606v1
#StructuralBiology #PyMOL #OpenScience
October 23, 2026 at 9:20 PM
🧬 Meet PROTFIG! An open-source tool for automatically generating publication-quality biomolecular figures with PyMOL.
🔗 github.com/AmericaChi/P...
🔗https://biorxiv.org/content/10.64898/2026.10.20.760606v1
#StructuralBiology #PyMOL #OpenScience
🔗 github.com/AmericaChi/P...
🔗https://biorxiv.org/content/10.64898/2026.10.20.760606v1
#StructuralBiology #PyMOL #OpenScience
His method, MORPH, to visualize variant frequency onto protein structure is available here github.com/lucaschestnu...
GitHub - lucaschestnuttree/MORPH: Mapping gnomAD missense-variant data onto structure predictions for visualization and analysis in PyMOL.
Mapping gnomAD missense-variant data onto structure predictions for visualization and analysis in PyMOL. - lucaschestnuttree/MORPH
github.com
October 21, 2026 at 2:04 PM
His method, MORPH, to visualize variant frequency onto protein structure is available here github.com/lucaschestnu...
Authors published a paper in Biorxiv, they used PyMOL in the study. Including #RRIDs will make this less ambiguous.
SciScore made a table with this resource, see “Automated Services” module (download as csv, xml or #jats) #RRID #methodsmatter
SciScore made a table with this resource, see “Automated Services” module (download as csv, xml or #jats) #RRID #methodsmatter
www.biorxiv.org
October 19, 2026 at 12:00 PM
Authors published a paper in Biorxiv, they used PyMOL in the study. Including #RRIDs will make this less ambiguous.
SciScore made a table with this resource, see “Automated Services” module (download as csv, xml or #jats) #RRID #methodsmatter
SciScore made a table with this resource, see “Automated Services” module (download as csv, xml or #jats) #RRID #methodsmatter
A collection of Python scripts for PyMOL
Jeremy Tame recently mentioned a python script to produce clickable Ramachandran plots, code is available on GitHub https://github.com/JezTame/pymol-rama His website also...
Jeremy Tame recently mentioned a python script to produce clickable Ramachandran plots, code is available on GitHub https://github.com/JezTame/pymol-rama His website also...
A collection of Python scripts for PyMOL
Jeremy Tame recently mentioned a python script to produce clickable Ramachandran plots, code is available on GitHub https://github.com/JezTame/pymol-rama His website also describes several other useful scripts http://www.tsurumi.yokohama-cu.ac.jp/pdl/PDL/PYTHON/index.html
macinchem.org
October 9, 2026 at 11:31 AM
A collection of Python scripts for PyMOL
Jeremy Tame recently mentioned a python script to produce clickable Ramachandran plots, code is available on GitHub https://github.com/JezTame/pymol-rama His website also...
Jeremy Tame recently mentioned a python script to produce clickable Ramachandran plots, code is available on GitHub https://github.com/JezTame/pymol-rama His website also...
OpenAI’s dot is a protein designer now 😂 It runs RFdiffusion/MPNN/AF2 on its cloud computer, tracks progress in a scratchpad, and opens the predicted designs in PyMOL to click through. All on CPU. Time to enter the Anthropic × Adaptyv competition with this setup? Wish me luck 😆
September 30, 2026 at 7:37 PM
OpenAI’s dot is a protein designer now 😂 It runs RFdiffusion/MPNN/AF2 on its cloud computer, tracks progress in a scratchpad, and opens the predicted designs in PyMOL to click through. All on CPU. Time to enter the Anthropic × Adaptyv competition with this setup? Wish me luck 😆
But the cool thing is: in the Cas12f:gRNA complex, the two N-termini of Cas12f already flank the gRNA. Thus if we fuse just *1* pdDronpa domain to the Cas12f NT, the pdDronpa dimer should form across the gRNA to cage it
Here's my manual model from 2021. No AF, no ML. Just PyMol.
Here's my manual model from 2021. No AF, no ML. Just PyMol.
September 29, 2026 at 5:16 PM
But the cool thing is: in the Cas12f:gRNA complex, the two N-termini of Cas12f already flank the gRNA. Thus if we fuse just *1* pdDronpa domain to the Cas12f NT, the pdDronpa dimer should form across the gRNA to cage it
Here's my manual model from 2021. No AF, no ML. Just PyMol.
Here's my manual model from 2021. No AF, no ML. Just PyMol.
Drop any AlphaFold 2/3, ColabFold, Boltz-2, Chai-1, OpenFold3, Protenix or ESMFold output (zipped is fine):
- iLIS next to ipSAE, pDockQ2, actifpTM…
- PAE and contact maps, chord diagrams
- Mol* 3D, ChimeraX/PyMOL scripts
- big complexes, reported PPIs (MIST + BioGRID)
- iLIS next to ipSAE, pDockQ2, actifpTM…
- PAE and contact maps, chord diagrams
- Mol* 3D, ChimeraX/PyMOL scripts
- big complexes, reported PPIs (MIST + BioGRID)
September 25, 2026 at 2:44 PM
Drop any AlphaFold 2/3, ColabFold, Boltz-2, Chai-1, OpenFold3, Protenix or ESMFold output (zipped is fine):
- iLIS next to ipSAE, pDockQ2, actifpTM…
- PAE and contact maps, chord diagrams
- Mol* 3D, ChimeraX/PyMOL scripts
- big complexes, reported PPIs (MIST + BioGRID)
- iLIS next to ipSAE, pDockQ2, actifpTM…
- PAE and contact maps, chord diagrams
- Mol* 3D, ChimeraX/PyMOL scripts
- big complexes, reported PPIs (MIST + BioGRID)
What PDB "chains" are and how to work with them in the PDB and PyMOL youtu.be/SVUzFO1rnZ0
What PDB "chains" are and how to work with them in the PDB and PyMOL
YouTube video by the bumbling biochemist
youtu.be
September 20, 2026 at 10:44 PM
What PDB "chains" are and how to work with them in the PDB and PyMOL youtu.be/SVUzFO1rnZ0
Authors published a paper in Biorxiv, they used PyMOL in the study. Including #RRIDs will make this less ambiguous.
SciScore made a table with this resource, see “Automated Services” module (download as csv, xml or #jats) #OpenScience #STMpublishing
SciScore made a table with this resource, see “Automated Services” module (download as csv, xml or #jats) #OpenScience #STMpublishing
www.biorxiv.org
September 21, 2026 at 12:00 PM
Authors published a paper in Biorxiv, they used PyMOL in the study. Including #RRIDs will make this less ambiguous.
SciScore made a table with this resource, see “Automated Services” module (download as csv, xml or #jats) #OpenScience #STMpublishing
SciScore made a table with this resource, see “Automated Services” module (download as csv, xml or #jats) #OpenScience #STMpublishing
In preparation of teaching a bioinformatics lab next week, I updated my PyMOL (molecular visualization software program) resources page including a PDF guide to PyMOL fundamentals. Hope it’s helpful!
thebumblingbiochemist.com/365-days-of-...
thebumblingbiochemist.com/365-days-of-...
September 17, 2026 at 1:42 AM
In preparation of teaching a bioinformatics lab next week, I updated my PyMOL (molecular visualization software program) resources page including a PDF guide to PyMOL fundamentals. Hope it’s helpful!
thebumblingbiochemist.com/365-days-of-...
thebumblingbiochemist.com/365-days-of-...
👓 Visualising sequence alignments in 3D?
Jalview enables multiple structures to be visualised with Chimera, ChimeraX, PyMOL and Jmol — helping scientists and educators bring biology to life.
📺 Explore the editor's functionality:
www.youtube.com/watch?v=pbms...
www.youtube.com/watch?v=yRBL...
Jalview enables multiple structures to be visualised with Chimera, ChimeraX, PyMOL and Jmol — helping scientists and educators bring biology to life.
📺 Explore the editor's functionality:
www.youtube.com/watch?v=pbms...
www.youtube.com/watch?v=yRBL...
September 15, 2026 at 9:33 AM
👓 Visualising sequence alignments in 3D?
Jalview enables multiple structures to be visualised with Chimera, ChimeraX, PyMOL and Jmol — helping scientists and educators bring biology to life.
📺 Explore the editor's functionality:
www.youtube.com/watch?v=pbms...
www.youtube.com/watch?v=yRBL...
Jalview enables multiple structures to be visualised with Chimera, ChimeraX, PyMOL and Jmol — helping scientists and educators bring biology to life.
📺 Explore the editor's functionality:
www.youtube.com/watch?v=pbms...
www.youtube.com/watch?v=yRBL...
Authors published a paper in Biorxiv, they used PyMOL in the study. Including #RRIDs will make this less ambiguous.
SciScore made a table with this resource, see “Automated Services” module (download as csv, xml or #jats) #methodsmatter #STMpublishing
SciScore made a table with this resource, see “Automated Services” module (download as csv, xml or #jats) #methodsmatter #STMpublishing
www.biorxiv.org
September 15, 2026 at 12:00 PM
Authors published a paper in Biorxiv, they used PyMOL in the study. Including #RRIDs will make this less ambiguous.
SciScore made a table with this resource, see “Automated Services” module (download as csv, xml or #jats) #methodsmatter #STMpublishing
SciScore made a table with this resource, see “Automated Services” module (download as csv, xml or #jats) #methodsmatter #STMpublishing
I just started playing arround with PyMol a bit. What you can see in these Images are screenshots of the Structure of Bromocriptine that is binding to the D2 Receptor. Understanding or even imagining the binding of molecules to Receptors is very difficutlt to […]
[Original post on mathstodon.xyz]
[Original post on mathstodon.xyz]
September 14, 2026 at 11:29 AM
I just started playing arround with PyMol a bit. What you can see in these Images are screenshots of the Structure of Bromocriptine that is binding to the D2 Receptor. Understanding or even imagining the binding of molecules to Receptors is very difficutlt to […]
[Original post on mathstodon.xyz]
[Original post on mathstodon.xyz]
Authors published a paper in Biorxiv, they used PyMOL in the study. Including #RRIDs will make this less ambiguous.
SciScore made a table with this resource, see “Automated Services” module (download as csv, xml or #jats) #reproducibility #STMpublishing
SciScore made a table with this resource, see “Automated Services” module (download as csv, xml or #jats) #reproducibility #STMpublishing
www.biorxiv.org
September 7, 2026 at 12:00 PM
Authors published a paper in Biorxiv, they used PyMOL in the study. Including #RRIDs will make this less ambiguous.
SciScore made a table with this resource, see “Automated Services” module (download as csv, xml or #jats) #reproducibility #STMpublishing
SciScore made a table with this resource, see “Automated Services” module (download as csv, xml or #jats) #reproducibility #STMpublishing
R/Rstudio, ImageJ/FIJI, PyMol, ApE, Zotero, OpenCode, Inkscape, OBS, Brave, Zoom.
Latest addition is Obsidian (tip from my colleagues), which is a gamechanger.
Latest addition is Obsidian (tip from my colleagues), which is a gamechanger.
September 4, 2026 at 5:05 PM
R/Rstudio, ImageJ/FIJI, PyMol, ApE, Zotero, OpenCode, Inkscape, OBS, Brave, Zoom.
Latest addition is Obsidian (tip from my colleagues), which is a gamechanger.
Latest addition is Obsidian (tip from my colleagues), which is a gamechanger.
Authors published a paper in Biorxiv, they used PyMOL in the study. Including #RRIDs will make this less ambiguous.
SciScore made a table with this resource, see “Automated Services” module (download as csv, xml or #jats) #reproducibility #methodsmatter
SciScore made a table with this resource, see “Automated Services” module (download as csv, xml or #jats) #reproducibility #methodsmatter
www.biorxiv.org
September 4, 2026 at 12:00 PM
Authors published a paper in Biorxiv, they used PyMOL in the study. Including #RRIDs will make this less ambiguous.
SciScore made a table with this resource, see “Automated Services” module (download as csv, xml or #jats) #reproducibility #methodsmatter
SciScore made a table with this resource, see “Automated Services” module (download as csv, xml or #jats) #reproducibility #methodsmatter
Authors published a paper in Biorxiv, they used PyMOL in the study. Including #RRIDs will make this less ambiguous.
SciScore made a table with this resource, see “Automated Services” module (download as csv, xml or #jats) #RRID #STMpublishing
SciScore made a table with this resource, see “Automated Services” module (download as csv, xml or #jats) #RRID #STMpublishing
www.biorxiv.org
September 3, 2026 at 12:00 PM
Authors published a paper in Biorxiv, they used PyMOL in the study. Including #RRIDs will make this less ambiguous.
SciScore made a table with this resource, see “Automated Services” module (download as csv, xml or #jats) #RRID #STMpublishing
SciScore made a table with this resource, see “Automated Services” module (download as csv, xml or #jats) #RRID #STMpublishing
Authors published a paper in Biorxiv, they used PyMOL in the study. Including #RRIDs will make this less ambiguous.
SciScore made a table with this resource, see “Automated Services” module (download as csv, xml or #jats) #methodsmatter #OpenScience
SciScore made a table with this resource, see “Automated Services” module (download as csv, xml or #jats) #methodsmatter #OpenScience
www.biorxiv.org
August 24, 2026 at 12:00 PM
Authors published a paper in Biorxiv, they used PyMOL in the study. Including #RRIDs will make this less ambiguous.
SciScore made a table with this resource, see “Automated Services” module (download as csv, xml or #jats) #methodsmatter #OpenScience
SciScore made a table with this resource, see “Automated Services” module (download as csv, xml or #jats) #methodsmatter #OpenScience
About 10% of our genome is regulatory DNA that tells when and how much of our genes are expressed. Proteins called transcription factors can enhance or inhibit segments so you make liver cells instead of heart cells in the right places. 📸 Emw/Wiki Commons/CC BY-SA 3.0
August 17, 2026 at 1:00 AM
About 10% of our genome is regulatory DNA that tells when and how much of our genes are expressed. Proteins called transcription factors can enhance or inhibit segments so you make liver cells instead of heart cells in the right places. 📸 Emw/Wiki Commons/CC BY-SA 3.0
The stick-like skeleton up top, the ribbon-like structure down below, huh, PyMol has been extended to the real world too? And, what's this molecule? lol?
August 15, 2026 at 11:30 PM
The stick-like skeleton up top, the ribbon-like structure down below, huh, PyMol has been extended to the real world too? And, what's this molecule? lol?