NTT DATA UCSF NIAID SEB Subcontract 2021 Task Order #2

March 1, 2021 - February 28, 2022 from ​Google Doc, continuation of NETE contract (Aug 2020 - Feb 2021).

1. General ChimeraX improvements to support NIAID (Eric: 20%)

2. Support the NIH 3D pipeline development, including any changes to ChimeraX to support ongoing development. (Eric: 15%)

3. Improve multi-person VR (Tom: 35%)
   1. Create video tutorials in how to use multi-person VR
   2. Hold VR office hours to train researchers to use VR capabilities
   3. Allow participants to add models from local files during a VR session
   4. Set up VR meeting servers for Africa, Europe, Asia

4. Human Biomolecular Atlas Program (HuBMAP) multiscale visualization (Eric: 30%)
   1. Develop ChimeraX tool to browse and select HuBMAP datasets for loading

5. Enhance ChimeraX’s segmentation capabilities
   1. Investigate increased use of simple ITK to support segmentation (Tom: 15%)
   2. Investigate utilizing web services to support more complex machine learning-based segmentation algorithms (Tom: 15%)
   3. Investigate reading and displaying segmentation format(s) available from imaging databases (tissue microscopy, cancer imaging data, etc.) (Tom: 10%)

6. DICOM (Tom: 25%, Eric: 5%)
   1. Improve ability to visualize and analyze medical images in VR with ChimeraX
   2. Develop browser-style interface to show DICOM dataset contents and associated metadata such as sample characteristics

7. Outreach
   1. Instructional material and tools documentation. (20%)
      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

8. Administration (10%)
   1. Submit monthly written reports of accomplishments

Meeting Minutes

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.

5/6/2021

Phil, Philip, Meghan, Darrell; Scooter, Elaine, Eric, Greg

Use of PDB or other databases' metadata in pipelines

For example, Eric's script uses the suggested contour level from an EMDB file. Meghan: another example is to look in the header to distinguish a virion from other viral proteins (Phil: this is in a record in the header) and direct them to different pipeline branches. Greg: metadata in scene export formats is which graphical object corresponds to which atom(s), but other metadata is best obtained from original data file, e.g. mmCIF/PDF.

Scooter: so you want to use existing metadata to influence pipeline processing... what about writing metadata into the GLTF/GLB? Phil: yes, maybe something like the structural hierarchy, overall complex -> different proteins -> chain descriptions, and which graphical objects correspond to each, similar to what Greg was describing. Greg: we would need to know what tags are required for the intended application (Enduvo, Phil says it's like powerpoint for VR, used in Uganda for training content, includes 2D assets like slides and 3D assets, movies, sound, evaluation questions).

Kristin is developing the Enduvo content with NIAID. We would like to talk directly to Kristin and Enduvo, primarily Greg to discuss what tags would be needed. Meghan and Phil: we will discuss with them and try to organize a collective meeting. Darrell: not sure which of these tasks are worth ChimeraX development. Need to strive for only what we think is highest value to both NIAID and ChimeraX user community. ChimeraX team can weigh in on what seems to be within our reasonable scope of effort. Scooter: seems worthwhile for export from ChimeraX to be showable in 3D web viewers. Meghan's idea: maybe have ChimeraX button to put the scene on NIH 3D, which would allow people to view it via the web there. Could have some limited interactivity using hierarchy metadata, e.g. turning chains on and off. Scooter: sounds like a great idea! Meghan: tradeoff between amount of metadata/interactivity in web viewer vs. file size, at some point (e.g. individual atom level) one should just use ChimeraX directly instead. (Meghan: conversely, going the other direction, could also have links from entries in NIH 3D to download the corresponding ChimeraX session files.)

Meghan likes the viewer and annotation tool in ​https://www.biodigital.com

Scooter: useful poster on glTF: ​https://kcoley.github.io/gLTF

Next time May 20: Kristin will be at the meeting

Time after that, June 3: maybe discuss PDB50 issues with Tef

5/20/2021

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

Kristin is showing her glb file 3D viewer made using babylon.js; surfaces colored by ESP and hydrophobicity, ribbons, atomic display, shadows, ambient occlusion, realistic lighting based on dome image (?), momentum spin, changing background color; she had to reduce meshes by ~80%

They are interested in metadata not only just in overall header but also in individual elements within the file.

TomG: now we have gltf export of vertex coloring, might add texture coloring. Kristin: not sure if mesh reduction can preserve texture. Many of the textures we use are black-and-white indicating where on surface a particular effect appears.

TomG: ChimeraX can write out an OBJ with uv texture coordinates and a texture image. Phil: if you provide OBJ with texture we can try it. TomG: I made these for Unity3D, will send something.

Phil: Would be useful to make models and chains as separate nodes in a hierarchy. Kristin: also grouping. Some programs like ZBrush flatten the hierarchy, but most others keep it (e.g. Maya).

Phil: Enduvo meeting last week; they want direct access to our 3D assets. Enduvo is like PowerPoint for VR. TomG: maybe we should try making an Enduvo lesson ourselves with models exported from ChimeraX with textures or vertex colors as needed. TomG: Can I get Enduvo? Phil: Cost is too high > $1000. Can introduce you to Enduvo developers. Also Enduvo is getting help from Unity developers, since it is a Unity app.

Kristen's babylon.js viewers (she wrote the Javascript) are here: ​https://3d-viewer-sandbox.s3.amazonaws.com/index.html

Tasks for TomG:

• provide instructions to export a colored molecule (atoms + ribbons) in OBJ with texture colors.
• allow models and chains to each be a distinct GLTF node.
• put textures for electrostatic coloring and hydrophobic coloring into GLTF output.

6/3/2021

Phil, Kristin, Philip, Megan, Eric, Greg, Scooter

Scooter's notes:

GLTF Metadata Ideas

• Which chains are included
• Ligand identification
• Which triangles are associated with which residue?
• Hierarchy
• Struts vs. molecular representation
• Also hydrogen bonds
• Labels
• Biological Unit

Conceptually easy to do, but we need to have agreement.

Suggestion: just do a pass and see what everyone thinks (Greg?)

UnityMol - FAIR share and interoperability of molecular models

Darrell: Scale

Idea: take advantage of the ​UnityMol pymol session reader to write a tool to import pymol sessions into ChimeraX

• Investigate and do some specification work in 4 weeks (after grant)

Eric's notes:

Phil, Philip, Kristin, Eric, Greg, Scooter, Meghan, Darrell

Greg: metadata from files vs. metadata in models. What can we add to metadata to help?

Phil: number of polygons in GLB output

Greg: could be determined from file. ChimeraX doesn't know ahead of time, would have to generate GLB and count.

Phil: what can you provide that isn't in mmCIF header?

Greg: hierarchy; h-bonds, struts

Phil: metadata may be used in Enduvo import

Greg: each GLB "object" can have a descriptive JSON dictionary associated

Meghan: if structs were labeled, they could be removed before handing to Enduvo

Phil: H-bonds if labeled, could be turned on/off easily

Scooter: time for a prototype; maybe make tags an option

Greg: file size not a real issue if hierarchy only to chains

Phil: are there standards for GLB JSON dictionaries

Greg: ad hoc, though there may be a few well known keys

Phil: ChimeraX GLB group names do show up when in Enduvo.

Greg: Those internal names could be improved.

Meghan: FAIR (reusable) scene depiction in mmCIF (​https://journals.iucr.org/d/issues/2021/06/00/qr5004/qr5004.pdf)

Scooter: Don't want each program to make its own "standard". But design by committee is slow.

Darrell: with 3D printed models, people tend to ask "what's the scale"?

Greg: may be able to use UnityMol's PyMOL session reading to read such sessions into ChimeraX(!)

NIH: that would be amazing; users have PyMOL sessions of what they want their structure to look like

Scooter: investigate feasibility -- come back to the PyMOL idea in 4 weeks (R01 renewal)

Greg: perhaps a subset

6/17/2021

Phil, Kristin, Philip, Darrell, Yong-Sok Lee (sp?); Tom G, Elaine, Eric, Greg

Tom G mentions potential hiring plans and infrastructure funding opportunities.

YS Lee's background is in computational chemistry, ligand design, QM, reaction mechanisms, may be interested in interfacing ChimeraX to GAMESS. Elaine mentioned the SEQCROW plugin to ChimeraX, Eric shared links to plugin and paper.

Tom G: what is ETA for dock prep? Eric: Dock Prep pieces (addh, charge calculations for nonstandard residues, swapaa to fix sidechains, altloc management) are available in ChimeraX but a lot of coding is needed to assemble them fully and create UI.

Tom G: Deep SSE Tracer is a machine-learning plugin developed by Jing He. We're interested in developing and interfacing with such machine-learning-related methods. Kristen: some are better than others, certainly. TG: CryoDRGN identifies multiple conformations in EM data. TG: we are also looking at using dimensionality-reduction approaches. In VR can reduce to 3D. Elaine: could think also about animating through time, using colors/sizes as additional dimensions, etc.

Kristen: question about exporting glb of an assembly of 6htx, gives an error. "index 1 is out of bounds" TG: it's a bug. Possible workaround is to use "sym" with "copies true" (requires more memory), but we should also fix the bug. The glb file could use instancing, but we are not writing it that way currently. Greg: should write glb with instancing. TG: yes, maybe as an option, but make it the default.

Phil:

• I attended a meeting and saw a poster on molecular dynamics optimization while user moves the ligand in VR, group at Bristol: ​https://gitlab.com/intangiblerealities/narupa-applications/narupa-imd
• Some issues with NIH-3D script dealing with NMR ensembles outputs whole thing when we'd just rather use the first conformation. Eric: send me an e-mail. Phil: OK!
• Enduvo has some issues with their glb reader, so let's wait until those are sorted out before sending them files from ChimeraX.
• Re export: PDB doesn't have total molecular weight, only per each entity. We remove waters and other stuff but would like export to include total molecular weight of atoms that are present (not including hydrogens or missing segments). Elaine: why not atom count instead? Darrell: let's re-examine the logic and then take a look at calculating what we need. Darrell: important thing is really the scale. TG: like dimensions in angstroms? Darrell: degree of magnification. Elaine: inherently angstroms, but we don't know how large it will be when 3D-printed. Greg: Blender units are meters. Phil: perhaps useful to export lengths of bounding box in X,Y,Z. Greg: we may need to improve our calculation of the global bounding box. Darrell: also may be rotated relative to the molecule. Elaine: how about measure inertia? But problem is that it doesn't enclose everything like a convex hull. Tom G: perhaps we can provide a similar command that encloses all atoms and/or surfaces. Phil: maybe we could use the ellipsoid to reorient the model along screen X,Y,Z. Tom G: maybe we can add the ability to ChimeraX to dump a separate XML or JSON file with the metadata instead of stuffing it all into the GLTF.

Philip: Want to run ChimeraX without accumulating history in a home directory, and also without contacting RBVI Toolshed server every fresh start. Greg: we need to add startup option to avoid phoning home. Also can make a temporary directory and set HOME environment variable to that directory so fetched files, file history, ... goes to that directory. TomG: should do more things with a "stateless" option, avoid reading/writing user data and settings. Eric: what about caching fetch data in ~/Downloads in stateless mode? TomG: Yeah, that is a problem.

7/01/2021

Phil, Philip, Darrell; Scooter, Tom G, Elaine, Eric, Greg

Scooter: our new hire Zach is coming soon

TomG recaps gltf export improvements: options to use instancing, texture colors. Now thinking about saving animations as gltf. Morph makes a large file, but maybe a protein can be defined as rigid subunits for skeletonization and "character animation." Examples: spike RBD up/down, prefusion vs. postfusion

Scooter: these are handled by babylon.js ... see also ​thin instances

Greg: ChimeraX startup options --exit and --script (and maybe --cmd, TBD) skip contacting the Toolshed

Phil: still evaluating what we need for figuring out molecule size/dimensions in the 3D pipeline

Phil: has wireless VR with Quest 2 to a desktop been tried with ChimeraX? TG: No. Quest 2 with tether works fine. Also we use Vive Pro with wireless adaptor. Phil: Vive wireless is not supported in Uganda because computers don't have a slot for the wireless card.

Phil: performance on Apple Silicon Macs? TG: we have a mac mini but not made a native ChimeraX for that cpu, am using Intel emulation, performance seems fine although native version could be faster. PyQT library not yet available for Apple Silicon. Some python benchmark reported as 3x faster on Apple M1 vs Apple Intel. Philip: Can't trust ARM vs Intel benchmarks. TG: We could benchmark python uses but have not yet. ChimeraX port to Apple M1 is probably at least 6 months away due to need for all third-party libraries to be ported.

Some discussion of how to temporarily change $HOME on linux with the unix "env" command. Philip: got around it by containerizing. Scooter: maybe should have $CHIMERAX_HOME. Greg: have ChimeraX create a temporary home (that gets removed).

7/15/2021

Phil, Philip, Meghan, Kristin; Elaine, Eric, Greg, TomG

Phil: will not be here next time; UCSF people are planning to be on campus 7/22.

Philip: 3D pipeline and ChimeraX playing well currently. Phil: helpful if ChimeraX could report molecular weight, w/o hydrogens for simplicity. Elaine: don't you want a "real" molecular weight with hydrogens? Phil: probably not much difference, just need to be up-front about how the number is calculated.

Tangents on 3D printing:

• ​Visualizing 3D imagery by mouth using candy-like models
• ​Computational design, fabrication and evaluation of rubber protein models

Meghan: working on surface coloring in GLB; Enduvo has issues with that. Another interesting app is ​IQ3Connect where instructor and students can share a session, similar to ChimeraX meetings but all works via browser and only one person can be the instructor. Also has issues with surface coloring in imported GLB, but sounds like they already know how to fix that. Phil: Can include movies, sound files, and go from scene to scene (different models). $200-$1000/month to enable hosting one meeting at a time (being the instructor and able to import models), free to join meeting. Meghan: interface is somewhat zoom-like, host can control permissions of the attendees.

We all tried joining a IQ3Connect meeting in web browser started by Phil. Meghan joined with Quest 2 headset (untethered). We can see a very shiny thick ribbon/stick model with stubby little avatars for the participants. They will explore this app further, are currently in a trial period.

Both IQ3Connect and Enduvo detect groups or subparts of the structure. TomG: ChimeraX gltf export makes a group for each model, submodel or drawing (e.g. atoms, ribbons, bonds) in ChimeraX, but does not separate chains.

TomG is interested in trying IQ3Connect with Phil and Meghan in VR on some realistic test case.

8/11/2021

Phil, Philip, Peter Steinbach, Anthony Armstrong, Kristen; Elaine, Eric, Greg, TomG, Zach, Scooter

Lately all the attention is on AlphaFold. TG described "alphafold match" and showed the 3p5b and 6vpv examples. Plans are to add "alphafold search" for when you don't have a structure, and blast search as alternative to current blat, and maybe eventually a service for running predictions. Also demo'ed Google colab.

Phil is interested in the use to fill in missing segments of experimental structures. AlphaFold was easier to use than other methods he tried and gave a reasonable conformation (based on other data) as the top hit.

Tony mentions ongoing tests using AlphaFold for building complexes, and a trick of putting U characters in the sequence to make linkers for a fusion protein. He also suggests an option to hide lower-confidence residues. Currently can be done with bfactor attribute specification.

Phil: a cautionary tale is progesterone receptor 1a28 alphafold match, you can see that multiple domains even within a monomer chain are not placed as expected relative to each other.

8/26/2021

Phil, Philip, Darrell (last 15 mins); Elaine, Eric, TomG, Zach

Philip: NIH3D pipeline is progressing, uses ChimeraX pubchem and EMDB fetch, mostly working well. Sent recent error message in chat for Eric to take a look.

Phil: found out your system was down when trying to file a ChimeraX bug report, that swapaa does not change sequence in Sequence Viewer. It's on Eric's todo list.

TomG: screenshare demo: uniprot features, alphafold GUI. Fetch (alphafold match) and AlphaFold Coloring panel. Corresponding commands show alphafold-generated residue attributes. Many options apply only when there is a corresponding experimental chain, will be grayed out. Search (alphafold search) runs blastprotein on the alphafold database. Predict (alphafold predict) runs Google Colab version of alphafold.

Will show warning that this notebook is from github (was not authored by Google); click button to run anyway. Requires Google account and initial sign-in. Sign-in may be retained by cookies depending on your browser settings. Next, HMMER, AlphaFold, and OpenMM are installed on a virtual machine. Then sequence databases are searched, a multiple sequence alignment generated, and the structure predicted. The entire process typically takes on the order of an hour or more.

Did not have time to show loop modeling, new capability just added as command, no GUI yet. Licensing issues may prevent NIAID from using Modeller, however.

9/8/2021 canceled

9/23/2021

Phil, Philip; Elaine, Eric, TomG, Zach

Now autostyling uses color bypolymer for models with 5-249 chains except for homomultimers, which still get color bychain.

Phil has been testing Eric's script on a variety of cases. Macromolecular pipeline (medium size) would like the default-sized ribbons for the nonprinting case, but also thickened ribbons with struts for the printing case. Small molecules ball-and-stick and CPK are fine for nonprinting, but sticks need to be thickened for the printing case. Few small glitches, one mol2 file failed, will send details. TG: have you tried tube helices? Phil: will take a look. We're not sure how they interact with struts. Other glitches: one virus color-by-chain didn't work, PDB file for zika virus capsid needs to get expanded to whole capsid; will send details. There was also a "volume" command issue but it may be fixed now.

When will your new 3D pipeline be publicly available? Phil: we may make a website that's not linked to anything but send people its URL for early access. Maybe early next year.

Phil: for visualization purposes, maybe we would be interested in all of an NMR ensemble as opposed to our current approach of using the first model only for everything.

Phil: EMDB will be changing their metadata schema. TomG: ChimeraX isn't using it yet anyway. Eric: the 3d pipeline script does use the recommended contour level. TomG: are there other interesting pieces of info? Phil: the corresponding PDB entry. TomG: maybe also resolution.

Phil: if you didn't yet, take a look at the stuff we prepared for the H3 Africa workshop. Areas with more advanced research include Uganda, Kenya, South Africa.

10/07/2021

Phil, Philip; Elaine, Eric, TomG, Zach, Scooter (first part)

Scooter showed vacation photos from his cabin (North woods area of Wisconsin). Maybe show more next time so that Darrell and Meghan can see.

Phil asked about AlphaFold getting more use after the 1.3 release. We plan to put a candidate on the download page next week.

Eric: four issues relating to 3D pipeline processing.

• Phil: outputs are all a fat ribbon with struts, but also wants a more normal ribbon for visualization. There are four ribbons with these printing changes, also want four more (with same colorings) that do not have these printing changes (fattening and struts). For small molecules, want another version of the sticks that is not so fat.
• 5ire virus generation, seems OK now.
• What colors to use for 7+ chains? Phil: can we have a palette repeat? Eric, yes among the other possibilities. Phil likes the interpolated one but wants to check with Darrell and get back to us. Tom G suggests doing something fancier based on symmetries, maybe as a longer-term goal. Phil: another fancy coloring is by domain.
• What to do when map level produces disconnected surface bits, with only a very small bit left after hide dust? Elaine: Doesn't that mean the level is wrong? Tom: may be correct level for step 1 but gets fragmented at the higher step automatically used for larger data. Even a single piece may be too fragile if it's a thin shell. Phil: printing software automatically thickens a too-thin shell. More discussion of just using step 1 (too many vertices is problematic for printing), map smoothing, iterating threshold adjustment vs. "measure volume" with "includeMasked false" (may be too slow). May need to leave this one to manual interactive adjustment. Chimera/X initial default is to put 1% of voxels inside contour. Tom G has fancier ideas like struts, or binning (e.g. bin 4 instead of step 4, more like smoothing, but requires also lowering threshold to avoid more fragmentation). Phil: measure volume of largest bit at step 1 vs 4, then possibly bin. Maybe enhance bin to use max instead of avg, then do that instead of adjusting step. TomG: needs evaluation; binning with max vs. avg may give more grid artifacts.

10/21/2021

Phil, Philip, Darrell, Meghan, Neta Filip-Granit (project manager for cryo-EM at NIAID); Elaine, Eric, TomG, Zach, Greg

Darrell: we may ask you about cryoEM issues in the future, since we know you're closely working with UCSF cryoEM folks. Neta: Recent advances include motion correction (Agard lab's MotionCor2), current challenge is data screening. TomG: EM is used in many different ways, including tomography. Please do ask more questions about this. Darrell: interested in how to archive data, how people revisit the same datasets.

UCSF team introduces itself.

Meghan: shouldn't we talk about progress on the 3D pipeline? Some emails went back and forth.

Philip: for EMDB it tries to get metadata (recommended threshold). Seems to be using FTP, is that for each entry? TomG: it chooses different locations. For Philip it is choosing the European site, ends up using FTP. TomG: will make a ticket to see if there is a newer https method available.

Philip: Some GLB files are causing errors. TomG: send example(s) please. We are not including texture coordinates, so it doesn't make sense that there is an error message complaining about them.

Elaine: other progress, Eric modified script to deal with structures missing many atoms, and correctly handle NMR ensembles. He also added a non-fattened ribbon output.

Phil: a couple of issues:

• EMDB is changing their data model, will stop supporting the current one in Feb 2022... will that cause problems, e.g. in getting the recommended threshold? Elaine: We haven't looked at what's changing yet, so can't say.

Tangents on recommended threshold:

• Philip: what else besides EMDB metadata could be used to help users set threshold? TomG: EMDB 3D viz tool Molstar, if they don't want to download/use ChimeraX. Maybe the NIH website could embed Molstar directly for this purpose, but you may have to feed it a reduced-size version of any huge maps. EMDB may already have reduced versions of such entries on their site.
• Darrell has used the EMDB-recommended threshold in Chimera/X and it didn't look the same as the EMDB picture, at least years ago, but as far as we know we haven't seen this problem. TomG: maybe they specified in sigma units rather than in the map raw units and that caused a mismatch.

Phil's other issue:

• problems with files that just have CA traces. Can we show ribbons for that? Elaine: yes... sent Phil with example image and CA-only PDB file.

Meghan posts link ​https://ds.litemol.org/ used for streaming in EMDB viewer (?)

Some discussion of AlphaFold vs. RosettaFold. Yifan Cheng tried connecting proteins with a linker and using AlphaFold but that did not predict the dimer correctly.

11/4/2021

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

What did they want to know about cryoEM? Workflow issues. Scooter: we should connect you with the UCSF Macromolecular Structure Group people including Matt Harrington. Darrell gave a EM crash course precently, including analogies to SEM, TEM, and cryoEM. Most structure "determination" includes some subjectivity.

Scooter: need to start thinking about the next year's contract soon. Let's start brainstorming in some meeting(s) soon, including what we did and didn't do from the previous contracts. Darrell: sounds good. Don't worry too much about the specifics, since plans have to evolve when other projects (E.g. hubmap) don't progress as expected.

Phil: By the way, I've seen others using ChimeraX recently, including for getting alphafold models. Are there any ongoing issues with the pipeline? Philip: not much, they have been resolved with fixes in daily build. Still have problems with FTP of EMDB maps. TomG: FTP is much better for general user populace (more reliable and faster), but I can add an option to use HTTPS instead, as long as you can tolerate extreme slowness in some cases. Will get it in next week. Discussion of whether recent changes for pipeline can go into 1.3 release or not... Eric will have to check on that.

Eric: Phil, did you and Darrell discuss the coloring of structures with >6 chains? Darrell: yes, but... may depend on situation, what you are trying to show. Phil: lean against "rainbow" [...] much discussion of coloring symmetry copies the same vs. color by entity (sequence) vs. color by polymer type vs. cycling through some standard palette of 6 colors vs. color by domain via UniProt features. Darrell: we can provide more alternatives for a given structure and allow users to choose which one(s) they want. Elaine: color by symmetry copies would require some new code. Darrell: we should ask our medical illustrator for advice on an expanded palette. Scooter, Elaine: try colorbrewer.org Elaine: these are already in ChimeraX (names can be used with the "palette" option of "color").

Eric will work on adding cycling thru palette and color bypolymer options, may examine coloring to avoid same color of contacting chains (no promises). Color tasks not assigned: color by domain, color by symmetry.

12/9/2021

Phil, Philip, Darrell, Meghan; Scooter, Elaine, Eric, TomG, Zach, Greg

Eric 3D pipeline updates: as mentioned in emails, has worked on script: EMDB fetch https, bypolymer coloring, fixed ensemble handling, map contour-surface adjustments.

Phil: vaccine res center wants SARS CoV-2 spike models, has been using Chimera because the whole 3D print process has been worked out more thoroughly. Also would be useful if ChimeraX vdw adjustment ("size" command) allowed incremental changes +/- current size instead of needing to specify absolute value.

Meghan: showed image of trimer 3D print for museum. Switched to epoxy instead of cyanoacrylate, is stronger. Still was hard to make it hold together, had to put white cylinder through the middle. Tom G: try ChimeraX tube helices. Could also make coil fatter.

• Custom Presets for 3D Print:

We should collaborate on a 3D print bundle for ChimeraX that adds custom presets with the settings that Phil likes. TomG and Scooter: should also make simpler Toolshed tutorials like one just for presets, and encourage more people to deposit their favorites. Elaine: analogous to COLOURlovers for palettes.

Meghan and Phil: could something malicious be placed in a ChimeraX session, and if so can we scan to check for them? Greg: .cxs is pure data like JSON but a custom bundle could execute the data. None of our bundles do that, but a 3rd-party one could. Another possibility is buffer overflow bug. Neither of those would be identified by scanning the session file.

• Possible Repository of ChimeraX Models/Sessions at NIH3D:

Meghan: Maybe we could have a repository of GLBs and/or ChimeraX session files at NIH 3D, with DOIs. Eric: Chimera has publish to sketchfab, maybe ChimeraX could have an analogous menu entry to publish to NIH3D. We don't know how much use this sketchfab thing has gotten. TomG: it involves a token, sends COLLADA. ChimeraX doesn't (yet) export COLLADA but we can add that if you need it and let us know. Elaine: are you worried about people sending you lots of junk that never gets used? Meghan, Phil: somewhat...

Eric: let's have the publish-to-NIH3D stuff in a bundle, then only people with real intent to use it will get it. That will prevent at least some of the random "what's this option? let me try it" junk.

Back to avoiding malicious code: TomG: we should add a way to scan for what bundles are referenced by a session file, and list them, or all nonstandard ones. Greg, Scooter: with option to ignore nonstandard bundles when loading a session. Eric: may not want to sanitize bundles against all 3rd-party bundles, e.g. ISOLDE may be important for published data with sessions.

Meghan: also need to consider selective permissions on data in the repository, e.g. people could only allow certain other people or themselves to access their data.

• AlphaFold update:

TomG: ChimeraX daily build now also interfaces to AlphaFold-Multimer for complexes (on Google Colab) although it's only possible for fairly small complexes. Has tutorial & video. ~800 residues in this complex, 5 hrs on Google Colab, ~2hrs on Wynton.

• VR update:

Phil: has tested ChimeraX VR on Oculus Quest2 with Airlink (w/o tether), works pretty well, plugging laptop in to power made a big difference. Need ethernet cord to laptop. Used Wifi 6 router. Easy to switch back and forth between tether and Airlink. Laptop graphics may be 2070, not sure. Greg: why can't signal go straight from laptop to Oculus instead of via router? Meghan: will need Meta account instead of Facebook account. Phil: I heard you can get them to switch now if you call and say you're having problems with Oculus connecting to your Facebook account. Walmart is selling refurbished Quest2 for $199.

• Next meeting? Darrell: how about Philip (and others from NIAID) presenting pipeline progess next week at the regular time.

12/16/2021

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

Phil is working (using Chimera) on 3D print of omicron variant spike for VRC. Icosahedrons show glycosylation sites. May need "ribbackbone" command. Looked into ChimeraX tube helices, but connections to coil look fragile. This 3D print will need lots of bracing.

Eric has added ChimeraX ability to change radii relative to current values.

Phil demo'd ChimeraX at a meeting with Jeremy Swanson and some other NIH people interested in VR & related, would TomG be willing to give them a VR demo in January? Will contact TG later with details.

Is unable to save Chimera session, problem with surface gneration. Maybe something to do with the struts? Elaine: or radius changes? Phil: changed radii back to default and still had the problem. Elaine: maybe try export to ChimeraX and switch over, and then regenerate icosahedrons. TomG: shape icosahedron command is same between Chimera and ChimeraX.

Phil: Chimera surface failure is disadvantage, but advantages are ribbon style gui, split/copy/combine/join, rename chains, renumber residues etc. ChimeraX may do some of these things via commands but it's harder to find. Elaine: May need to use ChimeraX setattr to change chain ID.

Eric has been working on a bundle of presets for NIH 3D. In progress, will send to Phil as a wheel for approval and eventually make it available on ToolShed.

AlphaFold Database approximately doubled in size (v2 compared to v1). Need ChimeraX 1.4 daily build, 1.3 doesn't know about v2. TomG: we got a new machine to run AlphaFold predictions.

Meghan: maybe in some future meeting we can hear what Zach's doing.

Next meeting: Jan 6.

1/6/2022

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

For subsequent funding, Darrell wants to put us back on his contract, which turns over at the end of February. Doesn't know who will be awarded the contract. Should get more clarity on that next week. Darrell: no-cost extension of NTT contract is a possibility if we need to do a bridge. Scooter will e-mail Darrell to continue discussion.

TomG asked whether the pandemic affected Darrell's research direction. Darrell: not so much, although other NIAID groups were heavily involved in clinical data management and vaccine clinical trials.

Potential areas for next contract:

• cryoEM: Drivers of interest are that it is increasingly important in structural biology in general, and NIAID has a core facility with a new and enthusiastic director, James Cherry.
• VR: Still very much of interest. Somewhat of a pause recently due to equipment requirements if used remotely, and pandemic-related decrease in users of their own VR facility.
• HubMap: somewhat of a falling-out with disorganized and demanding HubMap team. Visualizing/fetching HubMap data is still of interest, but they may not be directly engaged.

• Medical imaging: How much emphasis should we place on ChimeraX development in this area? Darrell: mainly interested in the context of VR, shared VR meetings. Phil: there may be fertile ground for ChimeraX development is segmentation in 3D in VR. 2D tools not so great for segmentation. Could also apply to 3D light microscopy, EM tomography, ...
• AlphaFold: we think many people are using these capabilities, not just new prediction but also fetch and sequence search of the database of existing structures. The database itself doesn't have this capability, so the ChimeraX interface is often more convenient. TomG: Google is not treating this as a product, it's more like academic software with little incentive for improvement. Should we include this AlphaFold usability stuff in the contract? Darrell: worthwhile, but consider whether it's a better fit for the R01. It could possibly be in the contract, as our mission includes democratizing the latest tools and methods. TomG: maybe better wording than "democratizing" is "diversity, equity, inclusion."

Eric made a bundle of many (~20) presets for NIH 3D pipeline. Phil has tried these, will provide feedback; not yet given to Philip to integrate in pipeline. Phil: looks like they're working well, but a couple are missing; will send Eric e-mail with details.

Philip: how will those be incorporated? Eric: if ChimeraX instance is persistent, run a command to install bundle when it is started. Philip: ChimeraX is installed at the beginning with the creation of the virtual machine.

Eric created ChimeraX tickets for renumbering residues, renaming chains. Join models is on the "todo" list. Copy/combine is already available.

1/20/2022

Phil, Philip, Meghan; Elaine, Eric, TomG, Greg, Zach

Discussion of Oculus Quest2 headset, its heaviness and straps. Freedom from a tether is a big advantage.

Can it be used offline (without logging in to Facebook)? Enterprise version doesn't require logging in to Facebook. Meghan: One facebook account can administer up to four devices. Tom: Or is it that one headset can attach to four facebook accounts? It may be both.

Tom has tried ChimeraX, Molecular Zoo, Beat Saber, VR ping-pong game on quest2. Intend to try Nanome. Body parts can block communication between headset and controllers. Phil: localization of controllers not as good as with vive lighthouse systems.

Discussion of when/whether we can be moved back to an MSC contract. Mechanism still in flux. Last time we talked about what could be in the next contract.

Phil has been trying AlphaFold. Tom is gathering statistics on run times.

NIH 3D presets from Eric: order of application is important. The order in the script currently works but different orders may produce different results (namely, the surface presets delete ligands etc. that are shown by some of the others). Phil: want non-fattened ribbon versions with coloring by chain and by rainbow. Need to consult with Meghan and Darrell on a few of them and get back to you later.

2/3/2022

Phil, Philip, Meghan; Elaine, Eric, TomG, Zach, Greg

Meghan says she has a list for us of stuff that would be useful in VR...

Philip says there are some 3D pipeline workflow changes but should not affect the ChimeraX part. Daily build will be best when the pipeline starts using them.

Phil has been testing the updated presets and we've gone back and forth. Most issues addressed, needs more thought on the NIAID side. Will try 3D printing rectangle vs. oval strand. Need to take a look at the "sides" parameter of "cartoon style."

Request 1: Phil would like to be able to save a session from within VR. (In Quest2 could use airlink to laptop that wasn't even in the same room! Rift was plugged into laptop at the time.) Maybe toolbar icon analogous to save-image icon. Maybe save a copy if the session already had a name. Or fill in Save dialog with a name that could contain timestamp or "Copy N", which could even be done specifically only in VR.

Discussion of problem in some Windows setups where ~/Desktop in output pathname is an unwritable location.

Meghan: is there some way to type on a virtual keyboard? TomG: SteamVR virtual keyboard enter key does not work. Scooter found something that says this bug has been fixed. TomG: jury is still out on speech recognition.

Request 2: Another need is popup showing what is under the pointer. Too computationally expensive to do continuously. Maybe add a button-click function. May like to see the chain info too, not just the residue and chain ID. Another request is a laser-beam pointer. TomG: already have label mode, another click turns it off. Scooter: is that good enough for Phil? Phil: if you don't have to click on the same spot to turn it off. Elaine: yes to turn off a specific label, but clicking in empty space turns them all off.

Request 3: Meghan: another request is a useful thing we saw in MolArt, converting amongst UniProt, PDB author residue numbers, and the other PDB residue numbers. MolArt actually renumbers according to which scheme you like. Greg: we only use the author numbering, not the internal PDB numbering. Phil: both are of interest. Elaine: maybe we could have a Renumber Residue tool (with equivalent commands) that allows switching amongst the 3 or user-specified like in Chimera. Eric: UniProt on demand, model-level setting of which numbering is used.

Phil: could you (TomG) present ChimeraX VR to the NIH virtual and augmented reality SIG? An hour long a couple weeks from now. Interests include all areas including molecules, medical imaging, etc. TomG: sounds fun.