NIAID SOW Proposed deliverables (based on 2 FTE), January 2020

August 1, 2020 - February 28 , 2021.

Original ​Google doc version. Earlier SOW draft. Extra 2.5 FTE deliverables.

1. Extensions to ChimeraX to support the NIH 3D pipeline
   1. Support the conversion of existing NIH 3D Print Exchange Chimera scripts to ChimeraX, advising on ChimeraX syntax for capabilities where available and noting missing features in ChimeraX where comparable features don’t exist
      1. Investigate using Smart Display
      2. Discuss Python vs. ChimeraX command line
   2. Implement essential missing features discovered above, including:
      1. PubChem fetch
      2. Additional import formats, including mol and sdf
      3. PDB biounit fetch #3515
   3. Sequence conservation coloring in ChimeraX
   4. Fetch sequence annotations (UniProt, domains, disease-associated mutations) (Eric)
      1. Automatic labels
   5. Enhancements to X3D export format (Greg)
      1. Look at GLTF export improvements (support for both per vertex coloring and texture coloring)
   6. Read and visualize segmentation models (see deliverable 2) (Tom)

2. Significantly enhance ChimeraX’s segmentation capabilities for 3d electron microscopy, light microscopy, and medical imaging
   1. Interactive SimpleITK use in ChimeraX (Tom)
   2. Allow loading, visualizing, creating, measuring and saving segmentations. (Tom)
   3. Support new EMDB-SFF segmentation file format from the EM Databank (Tom). #3639 in progress
   4. NOTE: some example data sets would be useful - AI Detected Lesions in lungs. Phil will get some data to TomG. Could also look at some data sets from SimpleITK. Bryan Hansen and Beth Fisher could also get some data sets

3. Medical imaging
   1. Metadata browser for DICOM files (Tom)
   2. Support radiologist collaborator needs by adapting ChimeraX to better suit standard workflows and to provide critical missing features identified by our collaborators (Tom)
      1. Need to get a collaborator
      2. Les Folio / Ron Summers
      3. New NIAID section focused on lung imaging
      4. Roberto Rodriguez Rubio, MD at UCSF director of ​Skull Base lab, interested in VR. Emphasis on dissections, no medical imaging.

4. Improve multi-person VR beyond work accomplished in 2019 SOW
   1. Localizable connection server solution - deliver a rendezvous server that can easily be deployed by institutions or enterprises. (Conrad/Greg)
      1. Fix cxconference TLS security #3629
      2. Get TLS certificate for plato cxconference server (Greg)
      3. Make cxconference work with VR #2892, #2893, #3498, #3512
      4. Greg to help containerize cxconference
5. Human Biomolecular Atlas Program (HuBMAP) multiscale visualization
   1. Engage with the HuBMAP group to evaluate the potential for ChimeraX extensions to support exploration and analysis of HuBMAP data, particularly as those extensions align with NIAID areas of interest. This will include determining the programmatic interfaces to access the HuBMAP data and initial efforts to scope the task of supporting the various HuBMAP data formats.
      1. Discuss needs with Meghan McCarthy and Darrell Hurt
6. Outreach
   1. Workshops, Training and presentations
   2. Instructional material and tools documentation.
      1. Detailed instructions for all features shall be provided in a user manual
      2. Written user guides and tutorials shall be available as an HTML page
7. Administration
   1. A project schedule, implementation plan, and documentation plan will be provided
   2. Monthly status reports detailing progress on each subtask will be delivered

Additional Requests from Users

1. Adding Coulombic coloring (Eric) #3596 (Elaine: this is one of the essential missing features mentioned in 1b above)
   1. 90% cases covered
2. Colada export for preparing models for PathogenAR cellphone app (Tom) #485
3. Add support for SDF V3000 (Eric)

Meeting Notes

Zoom meeting URL ​https://nih.zoomgov.com/j/1600907987

9/24/2020

Darrell Hurt, Phil Cruz, Meghan McCarthy, Scooter Moris, Greg Couch, Tom Goddard, Elaine Meng, Eric Pettersen

1. NIH 3D pipeline status
   1. they're working on the architecture, backend, using GLTF (.glb) rather than X3D
   2. Darrell: Philip will use ChimeraX as executable rather than reaching into python
   3. Scooter: how about REST interface approach with Json; are they interested?
   4. Darrell: makes sense, but need Philip to weigh in

2. VR meeting
   1. TomG, Phil, Victor tried 3-way meeting to work on firewall issues.
   2. Direct connection to TomG's home computer worked.
   3. AWS firewall mis-configured, test failed, will try again.
   4. Found several bugs in multiuser VR, created tickets. #3735, #3736, #3737, #3738, #3739, #3740, #3755.
   5. Discussed naming meetings using a rendezvous service, simplifying AWS setup, providing free AWS service hosted by NIAID or UCSF.

3. V3000 SDF support from Eric
   1. Phil is happy, allows them to jettison OpenBabel
   2. Elaine put this in Change Log dated Sept 15

4. macOS Big Sur
   1. TomG mentions ChimeraX fails to on macOS Big Sur beta, patched in daily build
   2. Phil says they aren't even at Catalina yet

5. VR hand tracking
   1. Darrell asks about VR hand-tracking, shows video of putting on gloves, PPE
   2. TomG has not looked at hand-tracking since the Leap device has poor tracking

10/08/2020

Darrell, Meghan, Phil, Philip, Kristen, Victor; Scooter, Greg, Elaine, Eric, TomG

• ChimeraX REST interface and Json output
  • Eric demo with GUI but can be done with script in nogui mode
  • "remotecontrol" to start REST, put URL shown in the ChimeraX Log into web browser; the resulting page allows entering commands and getting json replies, if any
  • currently Json output is implemented for "open" and "info" commands
  • would be useful for "info chain" to report polymer type in addition to whether there are any polymers
  • maybe we can provide a prototype python script to start rest, open structure, get information on chains and their types
  • Eric will improve user-error reporting in json

• VR experiment 1 wk ago with 4-way: Phil, Meghan, Victor, TomG via AWS
  • found more bugs, including "ghosts" (now fixed)
  • TomG recently added (Sep 30) features: new input model type ​photo (2D image, e.g. for showing a paper figure in VR) and new ​move picked model mouse mode to move models w/o having to select them first
  • TomG plans to add remembering the face image, name, and hand-cone color previously specified for VR meeting
  • worked pretty well on cheapest AWS tier
  • perhaps NIAID could provide the hub
  • Greg wonders about security; TomG mentions ssh tunneling, Scooter mentions generated password

10/22/2020

Darrell, Meghan, Phil, Philip, Kristen, Victor; Greg, Elaine, Eric, TomG

• Scooter on vacation for a month, sailing home from Mexico, returns Nov 22 (Elaine: this is approximate, weather-dependent)

NIH 3D pipeline:

• Eric working on converting workflow to ChimeraX
• Got 3 scripts from Phil Cruz
• TomG joined github repository for scripts set up by Philip; it seems that 2-factor authentication will not be a problem for our day-to-day work
• Eric: only few issues with the 2 shorter scripts
  • ChimeraX does not write VRML; not absolute requirement, can convert glb to vrml in separate step
  • ChimeraX "graphics quality" can be used to adjust numbers of triangles for STL output
  • no incremental radius adjustment a la Chimera vdwdefine plus/minus; Eric will supply python to do this
  • no combine, why was it used? Phil: to handle biological assemblies that were multiple models. Eric: now the fetch gets the assemblies as single models
• Philip asks about taking all the file reading and branching out of the ChimeraX scripts and instead have several separate ChimeraX scripts that are called; however, parsing with ChimeraX has several advantages
• Phil: actually may want to combine small-molecule and macromolecule scripts into one to reduce user error; distinction is presence of "standard residues" (biopolymer chains)
• Darrell: how about also combining with volume script, have ChimeraX identify if upload is map? Eric: should be doable, at least if filename has standard suffix
• Darrell: will also need to distinguish which database goes with an identifier for fetch purposes
• Tom: maybe run ChimeraX once to assess content, send feedback/questions to user, then run ChimeraX again for the processing
• Phil: if REST, is a hybrid approach possible? Could just do via REST without having to run ChimeraX twice
• Eric has improved error reporting in JSON

Topics not covered:

• VR meetings: firewalls, slow networks, 3 or 4 participants
  • Wrote documentation for setting up AWS server added to meeting command web page
  • David Liou has set up NIAID AWS server, will test tomorrow
  • Working on improved handling of low-bandwidth connections
  • Adding meeting command proxy options for simpler use of AWS

11/5/2020

Darrell, Phil, Philip, Kristen; Greg, Elaine, Eric, TomG, TomF

Pre-meeting agenda

NIH 3D pipeline:

• Eric transcribing print exchange scripts to ChimeraX
  • Improved performance with surfaces on large molecular complexes
  • fixed struts command making too many struts when used in script
• Studying how to handle level of detail for different use cases.
• Tested ChimeraX glTF of RNA on social VR platform Spatial
  • colors shown in Oculus Quest, but not in web browser.
• Is there an NIH 3D proposal the ChimeraX team can read?
• Is there a deadline for an initial pipeline prototype.

COVID PCR cellphone module:

• Kristen working on sars-cov-2 rna models, trying ChimeraX rna command.

VR meetings:

• Tested NIAID AWS meeting proxy with Phil and Victor with Phil hosting, all worked.
• Added name server:
  • start meeting "meeting start id covid-pcr"
  • join meeting "meeting id covid-pcr"
• Set up chimeraxmeeting.net domain for UCSF AWS meeting proxy and name server.
• Tried two simultaneous meetings on one AWS proxy server, worked fine.
• Made non-VR meeting participants see synchronized view direction.
• Improved session file compression using lz4 (4x smaller) to speed up joining meeting especially for low bandwidth connections.

Actual discussion

3D Pipeline:

Eric has translated the Chimera scripts into a single combined ChimeraX script that figures out processing path (small-mol, macromol, or map) from input file. Will get it to them via github.

Much discussion of control process, Phil notes that it is not always possible to discern whether one wants to treat an atomic structure as small or macro, so it will be necessary to allow user to specify which path to take.

Philip: why not always make all possible outputs for a given input? Don't worry about comp time or output size.

Phil: can present the user with gallery of outputs when they return to the website. Current process is not interactive, so not a problem if it takes several minutes.

TomG: hybrid approach, can ask user questions about what they want but also provide multiple alternatives.

What is their goal for revamping pipeline? First goal is to reproduce the Chimera outputs with similar from ChimeraX, except GLTF instead of X3D.

Darrell: re triangles, original goal was try to get a model that looked nice in graphics and was also suitable for 3D printing. Found that postprocessing decimation was better at maintaining appearance than decreasing triangles in Chimera; TomG: ChimeraX probably same, as we have not implemented fancy decimation or mesh repair.

Functionality is largely there, but implementations/parameters differ and will require some experimentation. E.g. ChimeraX does have a sym command with option to show surfaces, but the surfaces are calculated differently than in Chimera

VR meetings:

• TomG was able to run multiple meetings using same AWS virtual machine as proxy
• TomG added default meeting-name server chimeraxmeeting.net, but one can choose not to name the meeting, or use diff name server (will be saved in Prefs)
• Phil and Victor will test with low bandwidth; new session-compression will help

11/19/2020

Pre-meeting agenda

Darrell, Phil, Philip, Kristen, Meghan; Greg, Elaine, Eric, TomG, TomF

Eric cannot attend today.

3D Pipeline:

• Eric modified the ChimeraX pipeline script to allow specifying which branch to take (small mol, macromol, or map), or if not specified then chosen automatically. Regardless, the script reports what branch is used. He put the script on your github a couple of weeks ago. Feedback?

• Eric is working on porting addcharge to ChimeraX for a more complete implementation of coloring by Coulombic ESP

• Are there specific improvements to glTF output needed in ChimeraX?

VR Meetings:

• Phil, Victor and Meghan tried having two simultaneous two person meetings (one started by Phil, one by Tom) on the NIAID AWS server, last Friday. Worked with not noticeable slow down.

• New VR meeting user interface panel so no knowledge of the meeting command syntax is needed. Menu Tools / General / Meeting. Elaine has documented it.

• Meeting commands can now define multiple proxy servers.

Segmentation, Medical Imaging, HuBMAP:

• Our NIH 3D and VR meeting contract goals have made good progress. Which one of the 3 other areas, segmentation, medical imaging and HuBMAP would be best to get started? Are there BCBB projects we could assist on in these 3 areas?

Discussion

Darrell will be on a long road trip to Idaho, Colorado, Texas(?) in December for son's wedding and visit parents. Did not get exact dates.

3D Pipeline:

• Phil has tried the script, seems to work well in a few tests, needs to try with more data including edge cases and wider range of sizes
• The script looks for a recommended contour level for maps from EMDB, but some maps do not have this annotation
• NIH 3D Print Exchange will need Chimera 1.15 because of changes in RCSB PDB fetch
• Add new fetches?
  • Crystallography Open Database provides CIF, but ChimeraX does not read small-molecule CIF
  • ZINC provides formats ChimeraX reads (SDF, MOL2), we will reach out to Shoichet and/or Irwin

VR Meetings:

• Meghan: we will try a VR meeting with Uganda
• Victor: ...or with our own low-bandwidth test equipment
• the Meeting GUI is easier than using command, remembers multiple proxy servers
• TomG will investigate lowering the bandwidth requirement by using MessagePack library
• TomG wants to make a science-focused video also to publicize ChimeraX meeting capabilities

Segmentation, Medical Imaging, HuBMAP:

• re Hubmap, the contract was to investigate it rather than to implement specific visualization
• Kristen: may be too early to work with Hubmap, seems in flux
• Darrell: would still like to prioritize Hubmap
• Darrell: then secondarily, medical imaging; make use of ITK somehow? Would be strategic move to incorporate ITK. NIH has made investments in Hubmap and ITK, so using them may help subsequent round of funding.
• TomG: maybe work to make ChimeraX show DICOM simple ITK segmentations
• They will invite simple ITK developer(s) to our next meeting, Liv and Brad.

12/17/2020

VR meetings

• VR session with Uganda worked very well

Cytoscape for HuBMAP data

• Let's arrange for Scooter to demo scNetViz to the NIAID folks; see also ​recent Science paper in which a Cytoscape app is used to map genetic interactions onto structures in ChimeraX

Next contract

• We are drafting a task list for renewing the contract next year.

HuBMAP visualization

• Discussion of HubMap and ontologies.
• HubMap data has issues revealed in ChimeraX, like different brightnesses and z-planes for different tiles within the intestine data.
• Scooter knows Nils Gehlenborg (Harvard), maybe we could set up a meeting to discuss how ChimeraX can contribute to viewing HubMap data using capabilities beyond those in the portal. TomG would like more time to think about this (what exactly are the "beyond" capabilities: custom,in-depth analyses?) before we schedule a meeting.

HuBMAP anatomical models

• Kristen Browne talked about making anatomical organ models with Katy Borner for HuBMAP reference frame for positioning deposited samples.
• Katy has a person working on a VR placement tool.
• BCBB will have all the anatomical models in NIH 3D.

UniProt features in ChimeraX

• Eric has implemented getting sequence features from UniProt into ChimeraX, available in next daily build

Next meeting 1/14. Darrell returns January 11.

1/14/2021

Christopher Whalen (infrastructure, VR & other), Phil, Philip, Kristen, Darrell (at end of meeting); Scooter, Greg, Elaine, Eric, TomG

Scooter: we need to think about getting the next contract together soon. We will send a document with some possibilities.

Medical imaging: Got some helpful input from Gabriel Massano, Biomodelos 3D, Argentina

3D Pipeline status? Philip: has worked with VTK, but not yet workflow-ized the ChimeraX stuff. Phil plans to try Eric's script with edge cases, "normal" cases have worked well.

VR: Good performance in multisite meetings, even cross-country

Christopher: ​Bio-IT World journal interested in writing up the multiperson VR, African Centers for Excellence (ACE) initiative in Uganda and Mali. Article to focus on mission of ACE but would be interesting to include images and maybe even a video. Maybe there could be a "box" within the article focusing on ChimeraX. Scooter: let us know if/how we can help. Christopher: Uganda's internet is shut off right now... will talk to Rogers, the CEO of RENU, then we'll coordinate. Would be nice to involve the malaria-resistance project in Mali. Reporter may contact TomG. Scooter: the sooner the better.

Might be useful to make a Docker container or other container for VR server. Would just be sshd configuration with "GatewayPorts yes".

Darrell describes their old homology-modeling project (HaSP?) that showed structures in JSMol. New idea is apply to every viral spike protein, somehow involve Chimera(X). Scooter: REST interface? browse from within ChimeraX? ChimeraX processing and embedding into web page (WebGL, others?) Uniprot features mapping to 3D, glycosylation sites, etc.

1/28/2021

Phil, Philip, Meghan, Kristen, Darrell (first 40 mins); Scooter, Greg, Elaine, Eric, TomG

SOW proposal (NTT data)

Darrell: is it a la carte? Scooter: let's assume so for now, until/unless a problem of separability arises. (We view it on Phil's shared screen)

Darrell: they want monthly reports (invoices?)

Darrell/NIAID prioritization (unfortunately our copy is numbered differently):

• Highest: 2 (3d pipeline dev), 4 (multiperson VR), 8b (documentation), 9 (admin)
• High: 3a (investigate simple ITK), 5d (browse hubmap datasets, being able to visualize the data conveniently and without long setup)
• Medium: 1 (general NIAID use cases),3bc (seg web services, reading seg formats), 8a (workshops), 6 (dicom, depends on collaborator)
• Low: 5abc (additional hubmap viz tools e.g. data overlays like cell type on imaging, UI for clustering, light microscopy analysis), 7 ("hasp" homology modeling pipeline at their website)

TomG: I renumbered the google doc items this morning. Darrell listed the old numbering.

Scooter: 1 is the catchall allowing for tasks that are not anticipated, without having to change the contract. Therefore it is really in the "highest" category, and Darrell concurs.

TomG: segmentation is diff for diff applications (medical vs. cryoEM, light microscopy, etc.). Where is the emphasis?

Darrell: ITK has focused primarily on medical imaging, but the team is looking into using it on density etc. Would like to bring improvements from molecular viz into medical image analysis and vice versa. Separately, NIH is investing heavily cryoEM and related tools. Our own group's emphasis will segmentation as it applies to cryoEM.

Phil: use VR to view medical images along with their segmentations.

Darrell: Re the modeling pipeline, it's not yet approved, we're not sure it will happen. (Scooter: it can be put under 1, miscellaneous NIAID needs that arise.)

Darrell: Re DICOM and medical imaging, we should talk to Dr. Massano and any other expert users in that area and really find out how ChimeraX can contribute to the field, features they need, etc. Research-type clinicians. Phil: also surgeons, e.g. for surgery prep.

Phil: Do we need to meet sooner than Feb 11? Scooter: Let's continue communicating by e-mail in the meanwhile. Current contract ends mid-Feb. We aim to start next one end of Feb.

2/11/2021

Phil, Kristen, Darrell; Scooter, Greg, Elaine, Eric, TomG

SOW proposal (NTT data)

Viewing current document for task order "2" (continuation of current work order, so funding may actually start when the other ends mid-Feb). Darrell and Phil: content looks good.

Darrell: the monthly reports can be very simple; for ours, we just take development tracking notes and dump them into a document

Tom G: we're applying for "visual proteomics" funding from Chan-Zuckerberg Institute, enhancing VR for cell microscopy

Scooter: SOW contract is labor-only. If you have ideas for small equipment funding....

Darrell: if need be, we could purchase some hardware items and loan them to you as our collaborators

TomG: we don't know how ChimeraX VR works on the quest 2. Phil: Victor uses quest 1 at home, could provide information on that version of the headset.

Phil heard about a survey in which surgeons said they changed their surgical plans 20-25% of the time after using VR. TomG: I believe it's published.

There have been anecdotal (but significant) endorsements of insights from using VR by Bob Stroud and Tony Fauci.

TomG: hard to convince skeptics by what we write. The best way is to get people to actually use it, especially in cases that it benefits the most. Not all analyses need it.

Scooter: collect anecdotes, write a paper? Darrell: even host several datasets, say at NIH 3D. Phil:... or ​JoVE

2/25/2021

Phil, Kristen, Darrell (2nd half); Scooter, Greg, Elaine, Eric, TomG

Scooter: NTT data contract is signed! Starts 2/15. Working on February progress report.

Phil: ACE wants short movie demonstrating VR, hoping TomG can participate with making it sometime after daylight savings time starts (to help with Africa time difference). 1-2 min only showing people at different sites, not "how to use ChimeraX in VR" details but should include structures of some scientific interest.

Phil will attend Health Care VR 3 day virtual conference next week. ChimeraX VR was presented at this meeting 2 years ago. Not limited to clinical medicine VR.

Phil: tried Eric's pipeline scripts, worked well on all kinds of biounit examples. Having problems with x3d export of struts and hbonds, they are disconnected from ribbon. GLB export seems to be fine, appearance in ChimeraX also fine. Will send us a session and/or bug report.

Another difference is the "multiscale models" surface coloring and resolution e.g. for 1qqp. Copies of equivalent subunit are in different colors, and resolution values don't translate directly (need higher number in ChimeraX).

BioIT article on African Centers of Excellence is out. Darrell contributed text. Author did not contact ChimeraX team, focused on Africa resource challenges, but mentioned VR.

Darrell mentioned project organizing 1000 dicom images, cell histology and other data types. Likes ChimeraX ability to handle many data types.

3/12/2021

Phil, Philip, Darrell (2nd half); Elaine, Eric, TomG

Problem reported last time with strut disconnection in X3D exports has been fixed by Greg. Phil will test it.

Phil will try viral capsids with both a single combined surface and separate surfaces. Each may be preferred in different situations (e.g. coloring looks better with separate surfaces but they may cause 3D printing problems).

Use "graphics triangles" to report the number of triangles for better idea of export file size.

3D pipeline developers are thinking about parallelization of postprocessing. Multiple outputs for a single user input structure, may need to organize them by purpose (e.g. printing) in the interface or ask the user about purpose and then present the appropriate outputs.

We have been adding more GUIs to ChimeraX: volume tools, color key, etc. but still many more to go: dock prep, etc.

Phil asks about copy/combine functionality, not yet in ChimeraX. In the case of where the same model is split and then put back together, can instead use ChimeraX mouse mode rotate/translate selected atoms only.

Phil and Meghan want to know more about the SPOKE project and its data sources. Elaine will send them some links.

Darrell relaying concerns from people at Rocky Mt Lab that our interactions with them and with this NIAID in-house group might conflict (?) We aren't sure what this means.

Darrell suggests TomG or bigger ChimeraX team may visit NIH Bethesda for in-person collaboration and training similar to previous Chimera workshop at NIH.

Phil wants to try Virtual Desktop wireless VR with Quest 2 to PC with ChimeraX.

Next Wed 6 AM Phil will be training new postdoc in Mali to use VR. TomG can join VR meeting if desired. Will use Africa RENU VR server.

Phil attended VR in Public Health conference this week. VR will be in doctor's offices soon and has billable codes for insurance.

3/24/2021

Phil, Philip, Darrell; Elaine, Eric, TomG, Greg

Any progress on NIH3D pipeline as pertains to ChimeraX?

• Philip has incorporated the chimeraX unified py file into the workflow, says ChimeraX download from UCSF is slow. Error codes 64 (faulty usage) and 70 (internal software error) plus "expect trouble" (using gui. To avoid this, need to use nogui mode via --offscreen startup flag)
• Script calls sys.exit. Greg says zero/nonzero should be all you see, must be something with your workflow, and nonzero = error.
• NIH3D pipeline will be using cloud computing, currently not using systems with graphics hardware.
• offscreen rendering is currently slower, uses CPU rather than GPU. Can OSMESA use multiple CPU threads? Greg and possibly others will look into it.
• ambient lighting is slower, script already does size-dependent lighting
• Scooter: next step could be performance testing. Darrell's seen very slow examples with Chimera. Philip: let's try with ChimeraX, could well be different. Scooter: should try those specific examples, Phil will try to find them in the logs.

Did you want to know anything else about SPOKE?

• Phil: it was related to meeting with NASA re drug discovery to treat radiation effects
• NASA folks are combining lots of data types related to radiation effects (e.g. from exposure in space, nuclear accidents, etc.), including CT

VR stuff

• Phil reports problematic ChimeraX VR meeting with Mali last week; may have been internet connectivity to name server.
• TomG encourages use of "report a bug" and looping him in to meetings, in case he could help.
• Darrell: latency to Uganda was measured at ~350 milliseconds.
• Phil: how best to specify meeting proxy server? TomG: use Access menu in the Options of the GUI, but you have to use a command (meeting access? meeting settings?) to add a new server to the menu.
• TomG and Willan made a 60 minute long two-person VR video.
• we added a new ChimeraX videos page, includes some VR
• Video tutorials can play in ChimeraX help browser, at least on Mac, tested by Elaine.

4/8/2021

Phil, Philip, Meghan; Elaine, Eric, TomG, Scooter

Meghan: we've talked with an AR/VR group (​imisi3d.com) in Nigeria. They have downloaded and tried ChimeraX, and will do a remote meeting with NIAID folks, who will show them medical image data.

Phil: I have a collaboration with an investigator here to examine how two protein structures might interact, VR really helps with maintaining multiple constraints simultaneously. Also used HADDOCK protein-protein docking. Now have a compelling model of how hemoglobin and eNOS might fit together, will help guide peptide competition experiments. Steven Brooks et al., manuscript is in medarchive, will be submitted to Circulation.

Discussion of vaccines for influenza and covid-19 made by fusing viral proteins or their fragments to ferritin.

They have showed ChimeraX VR to "new guy" Wilbert van P and deputy director Jill Harper.

Tom G: would like to make a video showing multiperson AR/VR on SARS-CoV2 spike mutant(s). Would be great if Fauci could do it! Meghan: or get Fauci to do voiceover. Have been discussing similar with Barney (?)

ChimeraX 1.2 release is slated for end of month.

Tom G: will be working with Rodgers in Uganda to solve Mali VR meeting connection issues. SLAC also has firewall connection issues.

4/22/2021

Meghan, Philip, Darrell; Eric, TomG, Greg, Scooter

Network security

• Discussion of network breaches effecting NIH and UCSF.

NIH 3D giving users time estimates

• Good for users to know if job will takes 1 minute or 30 minutes
• Philip says another project (nefali?) output progress log, but no time estimates
• Tom says useful to get percent complete estimates for longest running step

X3D ChimeraX including meta data

• Greg Couch asked about including per-residue meta-data in X3D
• Meghan says want meta data for data attribution in GLB

Barney's covid-19 Chimera session file

• Meghan trying to use Chimera on spike model, Chimera session from Phil Cruz (on vacation), to help Barney (virus researcher)
• Chimera molecular surfaces failed on Windows
• Did not find a way to get it into ChimeraX.

Web 3D viewers

• For fastest 3d model network transmission, DRACO algorithm/format useful.
• Kristen Browne is working on a few 3D web viewers and should give a demo.
• Babylon.js web viewer, can drag and drop GLTF files for testing.