Well, it turns out that you can actually make PyMOL do quite a lot of stuff. Here's the full workflow, integrating the amazing ReGlyco into PyMOL to re-glycosylate the LDLA linker. There's some serious magic needed to get it running as fast as it is within PyMOL. @elisafadda.bsky.social
June 10, 2025 at 10:05 PM
Well, it turns out that you can actually make PyMOL do quite a lot of stuff. Here's the full workflow, integrating the amazing ReGlyco into PyMOL to re-glycosylate the LDLA linker. There's some serious magic needed to get it running as fast as it is within PyMOL. @elisafadda.bsky.social
A weekend project from a while back -- this little package (with no dependencies) allows you to interact with pymol remotely.
I use it a lot for my protein design workflows together with @biotite.bsky.social.
Just `pip install pymol-remote`
I use it a lot for my protein design workflows together with @biotite.bsky.social.
Just `pip install pymol-remote`
November 25, 2024 at 2:50 PM
A weekend project from a while back -- this little package (with no dependencies) allows you to interact with pymol remotely.
I use it a lot for my protein design workflows together with @biotite.bsky.social.
Just `pip install pymol-remote`
I use it a lot for my protein design workflows together with @biotite.bsky.social.
Just `pip install pymol-remote`
An FYI for people, PyMOL and pymol-open-source github.com/schrodinger/... are different
December 2, 2024 at 12:49 PM
An FYI for people, PyMOL and pymol-open-source github.com/schrodinger/... are different
Baker lab PyMOL config 👇
this is what we use:
set specular, 0
set ray_shadow, off
set antialias, 2
set ray_trace_mode, 1
set ray_trace_disco_factor, 1
set ray_trace_gain, 0.1
set ambient, 0.4
set direct, 0.45
set cartoon_sampling, 10
set ray_trace_color, black
set reflect, 1
set reflect_power, 0
set specular, 0
set ray_shadow, off
set antialias, 2
set ray_trace_mode, 1
set ray_trace_disco_factor, 1
set ray_trace_gain, 0.1
set ambient, 0.4
set direct, 0.45
set cartoon_sampling, 10
set ray_trace_color, black
set reflect, 1
set reflect_power, 0
April 28, 2025 at 6:56 AM
Baker lab PyMOL config 👇
Something I've been wondering is what sort of settings the Baker lab is using to get these gorgeous PyMOL figures with? (I'm assuming it's PyMOL?)
April 16, 2025 at 5:25 AM
Something I've been wondering is what sort of settings the Baker lab is using to get these gorgeous PyMOL figures with? (I'm assuming it's PyMOL?)
#alphafoldology in Pymol
I've created a new plugin for #PyMOL (called PyMOLfold) that allows you to fold protein sequences right in the GUI. Simply select your model of choice (e.g., #ESM3, Boltz-1) and paste in your amino acid sequence.
github.com/colbyford/Py...
#ai #proteinfolding #alphafold
github.com/colbyford/Py...
#ai #proteinfolding #alphafold
December 14, 2024 at 8:35 PM
#alphafoldology in Pymol
fyi - you can make very nice figures using PyMol with these custom settings (or modify them to make your own)
December 1, 2024 at 9:06 PM
fyi - you can make very nice figures using PyMol with these custom settings (or modify them to make your own)
Today we celebrate the life of Warren DeLano. Warren is best known for his development of PyMOL, the tool we use almost every day to depict 3D molecular structure of small molecules and proteins.
Please post your favourite PyMOL illustration. Tag with #PyMOL
#WarrenDeLano #PyMOL #Chemsky 🧪
Please post your favourite PyMOL illustration. Tag with #PyMOL
#WarrenDeLano #PyMOL #Chemsky 🧪
November 3, 2024 at 7:47 AM
Today we celebrate the life of Warren DeLano. Warren is best known for his development of PyMOL, the tool we use almost every day to depict 3D molecular structure of small molecules and proteins.
Please post your favourite PyMOL illustration. Tag with #PyMOL
#WarrenDeLano #PyMOL #Chemsky 🧪
Please post your favourite PyMOL illustration. Tag with #PyMOL
#WarrenDeLano #PyMOL #Chemsky 🧪
If u ever had to depict proteins as schematics in papers, u know the dilemma: how to create a pretty “blob”?
If structure ends up big & central, u’ll render it with PyMol et al, but for a truly schematic depiction u want a biorender-style icon, but for YOUR protein.
Think I’ve finally found a way.
If structure ends up big & central, u’ll render it with PyMol et al, but for a truly schematic depiction u want a biorender-style icon, but for YOUR protein.
Think I’ve finally found a way.
May 3, 2025 at 12:40 PM
If u ever had to depict proteins as schematics in papers, u know the dilemma: how to create a pretty “blob”?
If structure ends up big & central, u’ll render it with PyMol et al, but for a truly schematic depiction u want a biorender-style icon, but for YOUR protein.
Think I’ve finally found a way.
If structure ends up big & central, u’ll render it with PyMol et al, but for a truly schematic depiction u want a biorender-style icon, but for YOUR protein.
Think I’ve finally found a way.
Anyone know what program & settings was used to make these figs? I assume it isn't pymol or chimera (pic from @asimovpress.bsky.social on the other site)
August 17, 2025 at 8:16 PM
Anyone know what program & settings was used to make these figs? I assume it isn't pymol or chimera (pic from @asimovpress.bsky.social on the other site)
I've created a new plugin for #PyMOL (called PyMOLfold) that allows you to fold protein sequences right in the GUI. Simply select your model of choice (e.g., #ESM3, Boltz-1) and paste in your amino acid sequence.
github.com/colbyford/Py...
#ai #proteinfolding #alphafold
github.com/colbyford/Py...
#ai #proteinfolding #alphafold
December 13, 2024 at 1:46 PM
I've created a new plugin for #PyMOL (called PyMOLfold) that allows you to fold protein sequences right in the GUI. Simply select your model of choice (e.g., #ESM3, Boltz-1) and paste in your amino acid sequence.
github.com/colbyford/Py...
#ai #proteinfolding #alphafold
github.com/colbyford/Py...
#ai #proteinfolding #alphafold
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-...
September 23, 2025 at 8:16 PM
PyMol + Blender is cool. Learned this from @bradyajohnston.bsky.social
February 19, 2026 at 11:46 PM
PyMol + Blender is cool. Learned this from @bradyajohnston.bsky.social
Molecule-MCP is a very cool tool connecting PyMOL and ChimeraX directly to Claude through the Model Context Protocol for prompt-assisted molecule modelling. Great stuff by Jinyuan Sun et al
github.com/ChatMol/mole...
github.com/ChatMol/mole...
March 22, 2025 at 5:55 PM
Molecule-MCP is a very cool tool connecting PyMOL and ChimeraX directly to Claude through the Model Context Protocol for prompt-assisted molecule modelling. Great stuff by Jinyuan Sun et al
github.com/ChatMol/mole...
github.com/ChatMol/mole...
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
Update of my Pymol settings, including a bugfix
www.marcelswart.eu/blog/251201-...
Because life is too short for ugly images (and manual tinkering)
www.marcelswart.eu/blog/251201-...
Because life is too short for ugly images (and manual tinkering)
February 17, 2026 at 9:26 AM
Update of my Pymol settings, including a bugfix
www.marcelswart.eu/blog/251201-...
Because life is too short for ugly images (and manual tinkering)
www.marcelswart.eu/blog/251201-...
Because life is too short for ugly images (and manual tinkering)
For some more guidance on how to use this, Martin Buttenschön wrote a nice blogpost: www.blopig.com/blog/2024/11...
November 29, 2024 at 10:27 AM
For some more guidance on how to use this, Martin Buttenschön wrote a nice blogpost: www.blopig.com/blog/2024/11...
🚀 #CageCavityCalc Windows Installer is now available!
🔹 Automated Windows 64-bit installer (Win10 & 11)
🔹 Installs both CageCavityCalc plugin and PyMOL
🔹 Desktop shortcut for easy access
🔗 Download now at: github.com/VicenteMarti...
📰 doi.org/10.1021/acs....
More info 👇
🔹 Automated Windows 64-bit installer (Win10 & 11)
🔹 Installs both CageCavityCalc plugin and PyMOL
🔹 Desktop shortcut for easy access
🔗 Download now at: github.com/VicenteMarti...
📰 doi.org/10.1021/acs....
More info 👇
May 12, 2025 at 7:10 AM
🚀 #CageCavityCalc Windows Installer is now available!
🔹 Automated Windows 64-bit installer (Win10 & 11)
🔹 Installs both CageCavityCalc plugin and PyMOL
🔹 Desktop shortcut for easy access
🔗 Download now at: github.com/VicenteMarti...
📰 doi.org/10.1021/acs....
More info 👇
🔹 Automated Windows 64-bit installer (Win10 & 11)
🔹 Installs both CageCavityCalc plugin and PyMOL
🔹 Desktop shortcut for easy access
🔗 Download now at: github.com/VicenteMarti...
📰 doi.org/10.1021/acs....
More info 👇
Too cool to be true? 😎 Nope! GlycoShape ReGlyco runs on PyMol through the GlycoMe interface 🥰😍 check out this fab #glycotime tool from Hiren @glyco.me and Ojas @ojas-singh.bsky.social ⤵️🥳🥳🥳🎉🎉
Well, it turns out that you can actually make PyMOL do quite a lot of stuff. Here's the full workflow, integrating the amazing ReGlyco into PyMOL to re-glycosylate the LDLA linker. There's some serious magic needed to get it running as fast as it is within PyMOL. @elisafadda.bsky.social
June 11, 2025 at 6:33 AM
Too cool to be true? 😎 Nope! GlycoShape ReGlyco runs on PyMol through the GlycoMe interface 🥰😍 check out this fab #glycotime tool from Hiren @glyco.me and Ojas @ojas-singh.bsky.social ⤵️🥳🥳🥳🎉🎉
Week 4 of HTGAA (Protein Design) is done & I'm amazed!
I was always intimidated by 3D protein models in papers & never thought I'd understand them one day!
Today, I loaded a PDB file into PyMOL, saw the alpha helices & beta sheets of my Tyrosinase enzyme.
This is so cool. 🚀
#HTGAA #proteindesign
I was always intimidated by 3D protein models in papers & never thought I'd understand them one day!
Today, I loaded a PDB file into PyMOL, saw the alpha helices & beta sheets of my Tyrosinase enzyme.
This is so cool. 🚀
#HTGAA #proteindesign
November 11, 2025 at 2:27 AM
Week 4 of HTGAA (Protein Design) is done & I'm amazed!
I was always intimidated by 3D protein models in papers & never thought I'd understand them one day!
Today, I loaded a PDB file into PyMOL, saw the alpha helices & beta sheets of my Tyrosinase enzyme.
This is so cool. 🚀
#HTGAA #proteindesign
I was always intimidated by 3D protein models in papers & never thought I'd understand them one day!
Today, I loaded a PDB file into PyMOL, saw the alpha helices & beta sheets of my Tyrosinase enzyme.
This is so cool. 🚀
#HTGAA #proteindesign
Love PyMOL Remote, one of these tools that does one thing and does it well!
For some more guidance on how to use this, Martin Buttenschön wrote a nice blogpost: www.blopig.com/blog/2024/11...
November 29, 2024 at 11:28 AM
Love PyMOL Remote, one of these tools that does one thing and does it well!
Death to default PyMol color schemes (made with MN)
April 16, 2025 at 8:19 AM
Death to default PyMol color schemes (made with MN)