#chimerax — Public Fediverse posts

I put together a #ChimeraX plugin to display circos-like contact maps between proteins/DNA. I'm using it all the time now (after doing this manually for years) so I hope someone else may find it useful!

https://cxtoolshed.rbvi.ucsf.edu/apps/chimeraxcircoscontacts

https://circoscontacts.carltonlab.org

I put together a #ChimeraX plugin to display circos-like contact maps between proteins/DNA. I'm using it all the time now (after doing this manually for years) so I hope someone else may find it useful!

https://cxtoolshed.rbvi.ucsf.edu/apps/chimeraxcircoscontacts

https://circoscontacts.carltonlab.org

I put together a #ChimeraX plugin to display circos-like contact maps between proteins/DNA. I'm using it all the time now (after doing this manually for years) so I hope someone else may find it useful!

https://cxtoolshed.rbvi.ucsf.edu/apps/chimeraxcircoscontacts

https://circoscontacts.carltonlab.org

I put together a #ChimeraX plugin to display circos-like contact maps between proteins/DNA. I'm using it all the time now (after doing this manually for years) so I hope someone else may find it useful!

https://cxtoolshed.rbvi.ucsf.edu/apps/chimeraxcircoscontacts

https://circoscontacts.carltonlab.org

I put together a #ChimeraX plugin to display circos-like contact maps between proteins/DNA. I'm using it all the time now (after doing this manually for years) so I hope someone else may find it useful!

https://cxtoolshed.rbvi.ucsf.edu/apps/chimeraxcircoscontacts

https://circoscontacts.carltonlab.org

As invited, someone indeed came to our booth to see his own lipase #protein #structure project in #HoloDeck - fantastic! We prepared the file within a few minutes using #UCSF #ChimeraX and presented it in #AugmentedReality.
#DIYbio #lab #instruments #bioinformatics #CompChem #AR #education #STEM #MINT @tiltfive

As invited, someone indeed came to our booth to see his own lipase #protein #structure project in #HoloDeck - fantastic! We prepared the file within a few minutes using #UCSF #ChimeraX and presented it in #AugmentedReality.
#DIYbio #lab #instruments #bioinformatics #CompChem #AR #education #STEM #MINT @tiltfive

As invited, someone indeed came to our booth to see his own lipase #protein #structure project in #HoloDeck - fantastic! We prepared the file within a few minutes using #UCSF #ChimeraX and presented it in #AugmentedReality.
#DIYbio #lab #instruments #bioinformatics #CompChem #AR #education #STEM #MINT @tiltfive

As invited, someone indeed came to our booth to see his own lipase #protein #structure project in #HoloDeck - fantastic! We prepared the file within a few minutes using #UCSF #ChimeraX and presented it in #AugmentedReality.
#DIYbio #lab #instruments #bioinformatics #CompChem #AR #education #STEM #MINT @tiltfive

As invited, someone indeed came to our booth to see his own lipase #protein #structure project in #HoloDeck - fantastic! We prepared the file within a few minutes using #UCSF #ChimeraX and presented it in #AugmentedReality.
#DIYbio #lab #instruments #bioinformatics #CompChem #AR #education #STEM #MINT @tiltfive

I just tried the #Phenix integration in #ChimeraX, and it's so convenient!
Setup video + demo of the interactive use of phenix.douse here: https://www.youtube.com/watch?v=DlVgrQTZ5t8
It's really a great time to do atomic model building in #cryoEM maps! All the tools are getting really excellent.

I just tried the #Phenix integration in #ChimeraX, and it's so convenient!
Setup video + demo of the interactive use of phenix.douse here: https://www.youtube.com/watch?v=DlVgrQTZ5t8
It's really a great time to do atomic model building in #cryoEM maps! All the tools are getting really excellent.

I just tried the #Phenix integration in #ChimeraX, and it's so convenient!
Setup video + demo of the interactive use of phenix.douse here: https://www.youtube.com/watch?v=DlVgrQTZ5t8
It's really a great time to do atomic model building in #cryoEM maps! All the tools are getting really excellent.

I just tried the #Phenix integration in #ChimeraX, and it's so convenient!
Setup video + demo of the interactive use of phenix.douse here: https://www.youtube.com/watch?v=DlVgrQTZ5t8
It's really a great time to do atomic model building in #cryoEM maps! All the tools are getting really excellent.

Using #ChimeraX, I dock these #AF2 models into the map. I have seen a case with two different protein subunits of very similar sequences, which makes assigning each AF2 model to the density pretty difficult. It is however very easy to align (with the `matchmaker` command in ChimeraX) the AF2 models to the model produced by #model_angelo. This will unambiguously place similar AF2 models to where model_angelo detected their sequences.
5/19

Using #ChimeraX, I dock these #AF2 models into the map. I have seen a case with two different protein subunits of very similar sequences, which makes assigning each AF2 model to the density pretty difficult. It is however very easy to align (with the `matchmaker` command in ChimeraX) the AF2 models to the model produced by #model_angelo. This will unambiguously place similar AF2 models to where model_angelo detected their sequences.
5/19

Using #ChimeraX, I dock these #AF2 models into the map. I have seen a case with two different protein subunits of very similar sequences, which makes assigning each AF2 model to the density pretty difficult. It is however very easy to align (with the `matchmaker` command in ChimeraX) the AF2 models to the model produced by #model_angelo. This will unambiguously place similar AF2 models to where model_angelo detected their sequences.
5/19

Using #ChimeraX, I dock these #AF2 models into the map. I have seen a case with two different protein subunits of very similar sequences, which makes assigning each AF2 model to the density pretty difficult. It is however very easy to align (with the `matchmaker` command in ChimeraX) the AF2 models to the model produced by #model_angelo. This will unambiguously place similar AF2 models to where model_angelo detected their sequences.
5/19

Using #ChimeraX, I dock these #AF2 models into the map. I have seen a case with two different protein subunits of very similar sequences, which makes assigning each AF2 model to the density pretty difficult. It is however very easy to align (with the `matchmaker` command in ChimeraX) the AF2 models to the model produced by #model_angelo. This will unambiguously place similar AF2 models to where model_angelo detected their sequences.
5/19

Here are a few things I made and posted publicly in the hope they help others (will leave this pinned on my profile and update when relevant):

Visualizations with #ChimeraX: https://codeberg.org/Guillawme/chimerax-viz

"Quick copy a DOI" for #Zotero: https://codeberg.org/Guillawme/zotero-doi-link-quickcopy

A #Plutojl notebook to do non-linear curve fitting in #Julia: https://codeberg.org/Guillawme/julia-curve-fitting

A dump of slurm scripts, modulefiles and other things I used on different computers and clusters, mostly to do #cryoEM analysis: https://codeberg.org/Guillawme/cryoem-computing

Here are a few things I made and posted publicly in the hope they help others (will leave this pinned on my profile and update when relevant):

Visualizations with #ChimeraX: https://codeberg.org/Guillawme/chimerax-viz

"Quick copy a DOI" for #Zotero: https://codeberg.org/Guillawme/zotero-doi-link-quickcopy

A #Plutojl notebook to do non-linear curve fitting in #Julia: https://codeberg.org/Guillawme/julia-curve-fitting

A dump of slurm scripts, modulefiles and other things I used on different computers and clusters, mostly to do #cryoEM analysis: https://codeberg.org/Guillawme/cryoem-computing

Here are a few things I made and posted publicly in the hope they help others (will leave this pinned on my profile and update when relevant):

Visualizations with #ChimeraX: https://codeberg.org/Guillawme/chimerax-viz

"Quick copy a DOI" for #Zotero: https://codeberg.org/Guillawme/zotero-doi-link-quickcopy

A #Plutojl notebook to do non-linear curve fitting in #Julia: https://codeberg.org/Guillawme/julia-curve-fitting

A dump of slurm scripts, modulefiles and other things I used on different computers and clusters, mostly to do #cryoEM analysis: https://codeberg.org/Guillawme/cryoem-computing

Here are a few things I made and posted publicly in the hope they help others (will leave this pinned on my profile and update when relevant):

Visualizations with #ChimeraX: https://codeberg.org/Guillawme/chimerax-viz

"Quick copy a DOI" for #Zotero: https://codeberg.org/Guillawme/zotero-doi-link-quickcopy

A #Plutojl notebook to do non-linear curve fitting in #Julia: https://codeberg.org/Guillawme/julia-curve-fitting

A dump of slurm scripts, modulefiles and other things I used on different computers and clusters, mostly to do #cryoEM analysis: https://codeberg.org/Guillawme/cryoem-computing

Here are a few things I made and posted publicly in the hope they help others (will leave this pinned on my profile and update when relevant):

Visualizations with #ChimeraX: https://codeberg.org/Guillawme/chimerax-viz

"Quick copy a DOI" for #Zotero: https://codeberg.org/Guillawme/zotero-doi-link-quickcopy

A #Plutojl notebook to do non-linear curve fitting in #Julia: https://codeberg.org/Guillawme/julia-curve-fitting

A dump of slurm scripts, modulefiles and other things I used on different computers and clusters, mostly to do #cryoEM analysis: https://codeberg.org/Guillawme/cryoem-computing

I’m running my first script in #ChimeraX. Does this mean I am a structural biologist now?

I’m running my first script in #ChimeraX. Does this mean I am a structural biologist now?

I’m running my first script in #ChimeraX. Does this mean I am a structural biologist now?

I’m running my first script in #ChimeraX. Does this mean I am a structural biologist now?

I’m running my first script in #ChimeraX. Does this mean I am a structural biologist now?

Hmm that's not good. Won’t try that option again!

#IMOD #ChimeraX #microscopy

Hmm that's not good. Won’t try that option again!

#IMOD #ChimeraX #microscopy

Hmm that's not good. Won’t try that option again!

#IMOD #ChimeraX #microscopy

Hmm that's not good. Won’t try that option again!

#IMOD #ChimeraX #microscopy

Hmm that's not good. Won’t try that option again!

#IMOD #ChimeraX #microscopy

This is a nice summary on @focalplane_jcs of visualisation tools for 3D light #microscopy data.

https://focalplane.biologists.com/2023/06/14/community-collective-viewing-z-stacks-in-3d/

My go to is #ClearVolume or #ChimeraX (we steered clear of Imaris). Very interested to try out 3Dscript.

#CellBiology

This is a nice summary on @focalplane_jcs of visualisation tools for 3D light #microscopy data.

https://focalplane.biologists.com/2023/06/14/community-collective-viewing-z-stacks-in-3d/

My go to is #ClearVolume or #ChimeraX (we steered clear of Imaris). Very interested to try out 3Dscript.

#CellBiology

This is a nice summary on @focalplane_jcs of visualisation tools for 3D light #microscopy data.

https://focalplane.biologists.com/2023/06/14/community-collective-viewing-z-stacks-in-3d/

My go to is #ClearVolume or #ChimeraX (we steered clear of Imaris). Very interested to try out 3Dscript.

#CellBiology

This is a nice summary on @focalplane_jcs of visualisation tools for 3D light #microscopy data.

https://focalplane.biologists.com/2023/06/14/community-collective-viewing-z-stacks-in-3d/

My go to is #ClearVolume or #ChimeraX (we steered clear of Imaris). Very interested to try out 3Dscript.

#CellBiology

This is a nice summary on @focalplane_jcs of visualisation tools for 3D light #microscopy data.

https://focalplane.biologists.com/2023/06/14/community-collective-viewing-z-stacks-in-3d/

My go to is #ClearVolume or #ChimeraX (we steered clear of Imaris). Very interested to try out 3Dscript.

#CellBiology

I am still finding interesting things to do with protein #embeddings — now coloring #AlphaFold models by the 3-component UMAP reduction of the per-residue embedding. Look at those bright Phe residues in the disordered region — somehow #protT5 encodes them as "different" than the others.

In my experience so far these protein language models are uncannily able to highlight the same regions of the protein that I'm interested in already.

(#ChimeraX, using a sequence coloring format file)

I am still finding interesting things to do with protein #embeddings — now coloring #AlphaFold models by the 3-component UMAP reduction of the per-residue embedding. Look at those bright Phe residues in the disordered region — somehow #protT5 encodes them as "different" than the others.

In my experience so far these protein language models are uncannily able to highlight the same regions of the protein that I'm interested in already.

(#ChimeraX, using a sequence coloring format file)

I am still finding interesting things to do with protein #embeddings — now coloring #AlphaFold models by the 3-component UMAP reduction of the per-residue embedding. Look at those bright Phe residues in the disordered region — somehow #protT5 encodes them as "different" than the others.

In my experience so far these protein language models are uncannily able to highlight the same regions of the protein that I'm interested in already.

(#ChimeraX, using a sequence coloring format file)

@structbio

If you ever #dock models into noisy #cryoem maps, please look at the papers we (Claudia Millán, Airlie McCoy,
@terwilltom) have just released through bioRxiv!

# 1, theory:

https://www.biorxiv.org/content/10.1101/2022.12.20.521171v1

# 2, implementation in a program called EM_placement.

https://www.biorxiv.org/content/10.1101/2022.12.20.521188v1

Find it in today's (dev-4821) build of #Phenix (https://phenix-online.org/download/nightly_builds.cgi?show_all=1), and coming soon elsewhere including a #ChimeraX plugin!

@structbio

If you ever #dock models into noisy #cryoem maps, please look at the papers we (Claudia Millán, Airlie McCoy,
@terwilltom) have just released through bioRxiv!

# 1, theory:

https://www.biorxiv.org/content/10.1101/2022.12.20.521171v1

# 2, implementation in a program called EM_placement.

https://www.biorxiv.org/content/10.1101/2022.12.20.521188v1

Find it in today's (dev-4821) build of #Phenix (https://phenix-online.org/download/nightly_builds.cgi?show_all=1), and coming soon elsewhere including a #ChimeraX plugin!

@structbio

If you ever #dock models into noisy #cryoem maps, please look at the papers we (Claudia Millán, Airlie McCoy,
@terwilltom) have just released through bioRxiv!

# 1, theory:

https://www.biorxiv.org/content/10.1101/2022.12.20.521171v1

# 2, implementation in a program called EM_placement.

https://www.biorxiv.org/content/10.1101/2022.12.20.521188v1

Find it in today's (dev-4821) build of #Phenix (https://phenix-online.org/download/nightly_builds.cgi?show_all=1), and coming soon elsewhere including a #ChimeraX plugin!

@structbio

If you ever #dock models into noisy #cryoem maps, please look at the papers we (Claudia Millán, Airlie McCoy,
@terwilltom) have just released through bioRxiv!

# 1, theory:

https://www.biorxiv.org/content/10.1101/2022.12.20.521171v1

# 2, implementation in a program called EM_placement.

https://www.biorxiv.org/content/10.1101/2022.12.20.521188v1

Find it in today's (dev-4821) build of #Phenix (https://phenix-online.org/download/nightly_builds.cgi?show_all=1), and coming soon elsewhere including a #ChimeraX plugin!

@structbio

If you ever #dock models into noisy #cryoem maps, please look at the papers we (Claudia Millán, Airlie McCoy,
@terwilltom) have just released through bioRxiv!

# 1, theory:

https://www.biorxiv.org/content/10.1101/2022.12.20.521171v1

# 2, implementation in a program called EM_placement.

https://www.biorxiv.org/content/10.1101/2022.12.20.521188v1

Find it in today's (dev-4821) build of #Phenix (https://phenix-online.org/download/nightly_builds.cgi?show_all=1), and coming soon elsewhere including a #ChimeraX plugin!