<html><head><meta http-equiv="Content-Type" content="text/html; charset=utf-8"></head><body style="word-wrap: break-word; -webkit-nbsp-mode: space; line-break: after-white-space;" class="">Hi Gökhan,<div class=""><br class=""></div><div class=""> Your Nvidia RTX 3090 should give the best performance possible with current GPUs. There was a shortage of high-end graphics card in 2020 and supply continues to far outpace demand with popular cards priced 2 to 3 times their suggested retail price. For instance your RTX 3090 has a suggested price of $1500 but currently is priced over $3000. This may not improve until 2022 according to news reports. This may be the biggest problem in getting a new molecular visualization computer setup for VR.<br class=""><div class=""><br class=""></div><div class=""><span class="Apple-tab-span" style="white-space:pre"> </span><a href="https://www.theverge.com/2021/3/23/22345891/nvidia-amd-rtx-gpus-price-scalpers-ebay-graphics-cards" class="">https://www.theverge.com/2021/3/23/22345891/nvidia-amd-rtx-gpus-price-scalpers-ebay-graphics-cards</a></div><div class=""><br class=""></div><div class=""> I have not tried the HP Reverb G2 virtual reality headset. I know people were excited about the 2160 by 2160 pixels per eye resolution -- for comparison a Valve Index headset has 1440 by 1600 pixels. But reports said the hand-controller tracking with the Reverb G2 was below current VR standards. ChimeraX and any SteamVR application will work with any hand controllers. I have used ChimeraX VR with other Windows Mixed Reality controllers with a Samsung Odyssey headset with no problems. I've also used it with various other controllers with no problem: Vive Pro, Vive, Oculus Rift S, Oculus Rift, Oculus Quest. ChimeraX won't take advantage of the many extra inputs on Valve Index hand controllers.</div><div class=""><br class=""></div><div class=""> Nanome is a VR molecular visualization application funded by venture capital -- so they of course will need to charge plenty of money once that VC money runs out. I expect they will mostly be aiming their features at pharmaceutical company needs. I don't know if Nanome has any atomic model refinement capabilities.</div><div class=""><br class=""></div><div class=""> Tom</div><div class=""><br class=""></div><div class=""><br class=""><div><br class=""><blockquote type="cite" class=""><div class="">On Mar 23, 2021, at 12:11 AM, <<a href="mailto:tolung.bio@gmail.com" class="">tolung.bio@gmail.com</a>> <<a href="mailto:tolung.bio@gmail.com" class="">tolung.bio@gmail.com</a>> wrote:</div><br class="Apple-interchange-newline"><div class=""><div class="WordSection1" style="page: WordSection1; caret-color: rgb(0, 0, 0); font-family: Helvetica; font-size: 12px; font-style: normal; font-variant-caps: normal; font-weight: normal; letter-spacing: normal; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px; -webkit-text-stroke-width: 0px; text-decoration: none;"><div style="margin: 0cm; font-size: 11pt; font-family: Calibri, sans-serif;" class="">Hi Tom,<o:p class=""></o:p></div><div style="margin: 0cm; font-size: 11pt; font-family: Calibri, sans-serif;" class=""><o:p class=""> </o:p></div><div style="margin: 0cm; font-size: 11pt; font-family: Calibri, sans-serif;" class="">Thanks for the prompt response.<o:p class=""></o:p></div><div style="margin: 0cm; font-size: 11pt; font-family: Calibri, sans-serif;" class=""><o:p class=""> </o:p></div><div style="margin: 0cm; font-size: 11pt; font-family: Calibri, sans-serif;" class="">My responses are below.<o:p class=""></o:p></div><div style="margin: 0cm; font-size: 11pt; font-family: Calibri, sans-serif;" class=""><o:p class=""> </o:p></div><div style="margin: 0cm; font-size: 11pt; font-family: Calibri, sans-serif;" class="">Cheers,<o:p class=""></o:p></div><div style="margin: 0cm; font-size: 11pt; font-family: Calibri, sans-serif;" class=""><o:p class=""> </o:p></div><div style="margin: 0cm; font-size: 11pt; font-family: Calibri, sans-serif;" class="">Gökhan<o:p class=""></o:p></div><div style="margin: 0cm; font-size: 11pt; font-family: Calibri, sans-serif;" class=""><o:p class=""> </o:p></div><div style="margin: 0cm; font-size: 11pt; font-family: Calibri, sans-serif;" class=""><o:p class=""> </o:p></div><div style="margin: 0cm; font-size: 11pt; font-family: Calibri, sans-serif;" class=""><o:p class=""> </o:p></div><div class=""><div style="border-style: solid none none; border-top-width: 1pt; border-top-color: rgb(225, 225, 225); padding: 3pt 0cm 0cm;" class=""><div style="margin: 0cm 0cm 0cm 36pt; font-size: 11pt; font-family: Calibri, sans-serif;" class=""><b class=""><span lang="EN-US" class="">From:</span></b><span lang="EN-US" class=""><span class="Apple-converted-space"> </span>Tom Goddard <<a href="mailto:goddard@sonic.net" style="color: blue; text-decoration: underline;" class="">goddard@sonic.net</a>><span class="Apple-converted-space"> </span><br class=""><b class="">Sent:</b><span class="Apple-converted-space"> </span>Tuesday, 23 March 2021 5:49 PM<br class=""><b class="">To:</b><span class="Apple-converted-space"> </span><a href="mailto:tolung.bio@gmail.com" style="color: blue; text-decoration: underline;" class="">tolung.bio@gmail.com</a><br class=""><b class="">Cc:</b><span class="Apple-converted-space"> </span>Tristan Croll <<a href="mailto:tic20@cam.ac.uk" style="color: blue; text-decoration: underline;" class="">tic20@cam.ac.uk</a>>; ChimeraX Users Help <<a href="mailto:chimerax-users@cgl.ucsf.edu" style="color: blue; text-decoration: underline;" class="">chimerax-users@cgl.ucsf.edu</a>>; Simon Brown <<a href="mailto:simonb@uow.edu.au" style="color: blue; text-decoration: underline;" class="">simonb@uow.edu.au</a>>; James Bouwer <<a href="mailto:jbouwer@uow.edu.au" style="color: blue; text-decoration: underline;" class="">jbouwer@uow.edu.au</a>><br class=""><b class="">Subject:</b><span class="Apple-converted-space"> </span>Re: [chimerax-users] VR Support<o:p class=""></o:p></span></div></div></div><div style="margin: 0cm 0cm 0cm 36pt; font-size: 11pt; font-family: Calibri, sans-serif;" class=""><o:p class=""> </o:p></div><div style="margin: 0cm 0cm 0cm 36pt; font-size: 11pt; font-family: Calibri, sans-serif;" class="">Hi Gökhan,<o:p class=""></o:p></div><div class=""><div style="margin: 0cm 0cm 0cm 36pt; font-size: 11pt; font-family: Calibri, sans-serif;" class=""><o:p class=""> </o:p></div></div><div class=""><div style="margin: 0cm 0cm 0cm 36pt; font-size: 11pt; font-family: Calibri, sans-serif;" class=""> ISOLDE works in VR in a minimal way -- you can tug on atoms. Here's a little video showing that in ChimeraX 1.1.<o:p class=""></o:p></div></div><div class=""><div style="margin: 0cm 0cm 0cm 36pt; font-size: 11pt; font-family: Calibri, sans-serif;" class=""><o:p class=""> </o:p></div></div><div class=""><div style="margin: 0cm 0cm 0cm 36pt; font-size: 11pt; font-family: Calibri, sans-serif;" class=""><span class="apple-tab-span"> <span class="Apple-converted-space"> </span></span><a href="https://www.rbvi.ucsf.edu/chimerax/data/isolde-vr-mar2021/isolde_vr.mp4" style="color: blue; text-decoration: underline;" class="">https://www.rbvi.ucsf.edu/chimerax/data/isolde-vr-mar2021/isolde_vr.mp4</a><o:p class=""></o:p></div><div class=""><div style="margin: 0cm 0cm 0cm 36pt; font-size: 11pt; font-family: Calibri, sans-serif;" class=""><o:p class=""> </o:p></div></div><div class=""><div style="margin: 0cm 0cm 0cm 36pt; font-size: 11pt; font-family: Calibri, sans-serif;" class="">I turned off depth cue and clipping with commands "light depthcue off" and "clip off" otherwise it clips to a slab which keeps moving as I move my head. I click a VR button on the ISOLDE panel tug atoms mouse mode icon to assign the VR button. I wouldn't say this makes ISOLDE usable in VR. For instance I don't have a way to move the roaming contour mesh region which normally stays in the middle of the screen. But it is enough to play around a bit. I was using a GTX 1080 Ti graphics card. Both the VR and ISOLDE molecular dynamics are running on the graphics card so this puts heavy demand on the card. For simulating just a region around a residue it was reasonably smooth.<o:p class=""></o:p></div><div style="margin: 0cm; font-size: 11pt; font-family: Calibri, sans-serif;" class=""><o:p class=""> </o:p></div><div style="margin: 0cm; font-size: 11pt; font-family: Calibri, sans-serif;" class=""><span style="color: red;" class="">Thanks for the tips to get it to work with ISOLDE. I have a 3090 to play with (which recently replaced my trusty 1080) that should have significantly better performance than the 1080 Ti. Let’s see how it goes…<o:p class=""></o:p></span></div></div><div class=""><div style="margin: 0cm 0cm 0cm 36pt; font-size: 11pt; font-family: Calibri, sans-serif;" class=""><o:p class=""> </o:p></div></div><div class=""><div style="margin: 0cm 0cm 0cm 36pt; font-size: 11pt; font-family: Calibri, sans-serif;" class="">I would like to make ISOLDE work well in VR. I think it is the perfect VR application where you really benefit from the best 3D perception possible and the 6-degree-of-freedom hand controllers for moving atoms around is much better suited than a mouse.<o:p class=""></o:p></div><div style="margin: 0cm; font-size: 11pt; font-family: Calibri, sans-serif;" class=""><o:p class=""> </o:p></div><div style="margin: 0cm; font-size: 11pt; font-family: Calibri, sans-serif;" class=""><span style="color: red;" class="">ABSOLUTELY, and I cannot wait for that day that I’ve been waiting for since I started working on structures, to come…<o:p class=""></o:p></span></div></div><div class=""><div style="margin: 0cm 0cm 0cm 36pt; font-size: 11pt; font-family: Calibri, sans-serif;" class=""><o:p class=""> </o:p></div></div><div class=""><div style="margin: 0cm 0cm 0cm 36pt; font-size: 11pt; font-family: Calibri, sans-serif;" class="">VR resolution has not been a major issue for use in molecular visualization. We have been using Vive Pro headsets that have adequate resolution for a few years now. A Valve Index headset is probably the best choice for molecular visualization right now. People also use Quest 2 with link cable.<o:p class=""></o:p></div><div style="margin: 0cm; font-size: 11pt; font-family: Calibri, sans-serif;" class=""><o:p class=""> </o:p></div><div style="margin: 0cm; font-size: 11pt; font-family: Calibri, sans-serif;" class=""><span style="color: red;" class="">I have an HP Reverb G2 that recently replated my original HTC Vive. I am quite disappointed with it so far, and was wondering whether I should’ve gone for an Index. However, Index is not sold in Australia (and therefore would have required having one shipped from the US, which means no warranty here and expensive shipping). That was one of the reasons for going for the G2, and I have already used that warranty, since the first unit they sent died after minutes of first use!<o:p class=""></o:p></span></div><div style="margin: 0cm; font-size: 11pt; font-family: Calibri, sans-serif;" class=""><span style="color: red;" class=""><o:p class=""> </o:p></span></div><div style="margin: 0cm; font-size: 11pt; font-family: Calibri, sans-serif;" class=""><span style="color: red;" class="">Do you think ChimeraX+ISOLDE should work with the WMR controllers that come with the G2, or is the current code specific to the Vive controllers?<o:p class=""></o:p></span></div></div><div class=""><div style="margin: 0cm 0cm 0cm 36pt; font-size: 11pt; font-family: Calibri, sans-serif;" class=""><o:p class=""> </o:p></div></div><div class=""><div style="margin: 0cm 0cm 0cm 36pt; font-size: 11pt; font-family: Calibri, sans-serif;" class=""> The big problem is it would take many developer years of effort to have decent user interfaces in VR. The furthest along on this for molecular visualization is Nanome -- you should check out their molecular VR. We continued to develop ChimeraX VR including multi-person VR.<o:p class=""></o:p></div><div style="margin: 0cm; font-size: 11pt; font-family: Calibri, sans-serif;" class=""><o:p class=""> </o:p></div><div style="margin: 0cm; font-size: 11pt; font-family: Calibri, sans-serif;" class=""><span style="color: red;" class="">I have used Nanome’s one of the earliest versions, but it looks like they’re locking more and more of its features for free users based on my most recent try.<span class="Apple-converted-space"> </span></span><span style="font-family: "Segoe UI Emoji", sans-serif; color: red;" class="">☹</span><span style="color: red;" class=""><span class="Apple-converted-space"> </span>Does it work as well as ChimeraX+ISOLDE in refining models?<o:p class=""></o:p></span></div></div><div class=""><div style="margin: 0cm 0cm 0cm 36pt; font-size: 11pt; font-family: Calibri, sans-serif;" class=""><o:p class=""> </o:p></div></div><div class=""><div style="margin: 0cm 0cm 0cm 36pt; font-size: 11pt; font-family: Calibri, sans-serif;" class=""><span class="apple-tab-span"> <span class="Apple-converted-space"> </span></span>Tom<o:p class=""></o:p></div></div><div class=""><div style="margin: 0cm 0cm 0cm 36pt; font-size: 11pt; font-family: Calibri, sans-serif;" class=""><o:p class=""> </o:p></div></div><div class=""><div style="margin: 0cm 0cm 0cm 36pt; font-size: 11pt; font-family: Calibri, sans-serif;" class=""><o:p class=""> </o:p></div></div><div class=""><div style="margin: 0cm 0cm 0cm 36pt; font-size: 11pt; font-family: Calibri, sans-serif;" class=""><br class=""><br class=""><o:p class=""></o:p></div><blockquote style="margin-top: 5pt; margin-bottom: 5pt;" class="" type="cite"><div class=""><div style="margin: 0cm 0cm 0cm 36pt; font-size: 11pt; font-family: Calibri, sans-serif;" class="">On Mar 22, 2021, at 9:18 PM, <<a href="mailto:tolung.bio@gmail.com" style="color: blue; text-decoration: underline;" class="">tolung.bio@gmail.com</a>> <<a href="mailto:tolung.bio@gmail.com" style="color: blue; text-decoration: underline;" class="">tolung.bio@gmail.com</a>> wrote:<o:p class=""></o:p></div></div><div style="margin: 0cm 0cm 0cm 36pt; font-size: 11pt; font-family: Calibri, sans-serif;" class=""><o:p class=""> </o:p></div><div class=""><div class=""><div style="margin: 0cm 0cm 0cm 36pt; font-size: 11pt; font-family: Calibri, sans-serif;" class="">Hello Tristan and the Chimera team,<o:p class=""></o:p></div></div><div class=""><div style="margin: 0cm 0cm 0cm 36pt; font-size: 11pt; font-family: Calibri, sans-serif;" class=""> <o:p class=""></o:p></div></div><div class=""><div style="margin: 0cm 0cm 0cm 36pt; font-size: 11pt; font-family: Calibri, sans-serif;" class="">I have been using ChimeraX in VR: fantastic!<o:p class=""></o:p></div></div><div class=""><div style="margin: 0cm 0cm 0cm 36pt; font-size: 11pt; font-family: Calibri, sans-serif;" class=""> <o:p class=""></o:p></div></div><div class=""><div style="margin: 0cm 0cm 0cm 36pt; font-size: 11pt; font-family: Calibri, sans-serif;" class="">However, ISOLDE was not working in VR, unfortunately.<o:p class=""></o:p></div></div><div class=""><div style="margin: 0cm 0cm 0cm 36pt; font-size: 11pt; font-family: Calibri, sans-serif;" class=""> <o:p class=""></o:p></div></div><div class=""><div style="margin: 0cm 0cm 0cm 36pt; font-size: 11pt; font-family: Calibri, sans-serif;" class="">Is there a fix/workaround currently available to get ISOLDE running in VR?<o:p class=""></o:p></div></div><div class=""><div style="margin: 0cm 0cm 0cm 36pt; font-size: 11pt; font-family: Calibri, sans-serif;" class=""> <o:p class=""></o:p></div></div><div class=""><div style="margin: 0cm 0cm 0cm 36pt; font-size: 11pt; font-family: Calibri, sans-serif;" class="">Is there ongoing work on making ISOLDE VR compatible?<o:p class=""></o:p></div></div><div class=""><div style="margin: 0cm 0cm 0cm 36pt; font-size: 11pt; font-family: Calibri, sans-serif;" class=""> <o:p class=""></o:p></div></div><div class=""><div style="margin: 0cm 0cm 0cm 36pt; font-size: 11pt; font-family: Calibri, sans-serif;" class="">Also: 1) are there any advantages of using a Quadro card over a consumer-line card for ChimeraX VR? and 2) is there a recommended minimum system spec for getting high-enough frame rates in VR with large models? We are planning to put together a new system soon for molecular visualization and modelling, hence the questions.<o:p class=""></o:p></div></div><div class=""><div style="margin: 0cm 0cm 0cm 36pt; font-size: 11pt; font-family: Calibri, sans-serif;" class=""> <o:p class=""></o:p></div></div><div class=""><div style="margin: 0cm 0cm 0cm 36pt; font-size: 11pt; font-family: Calibri, sans-serif;" class="">Now that there are VR headsets with high-enough resolution (such as the HP Reverb G2) that allow reading smaller text and finer details in VR, I am hoping that the molecular visualization and modelling software will start providing built-in easy-to-use support for these devices. I applaud ChimeraX team for leading in this space (no pun intended<span class="apple-converted-space"> </span><span style="font-family: "Segoe UI Emoji", sans-serif;" class="">😊</span>).<o:p class=""></o:p></div></div><div class=""><div style="margin: 0cm 0cm 0cm 36pt; font-size: 11pt; font-family: Calibri, sans-serif;" class=""> <o:p class=""></o:p></div></div><div class=""><div style="margin: 0cm 0cm 0cm 36pt; font-size: 11pt; font-family: Calibri, sans-serif;" class="">Best,<o:p class=""></o:p></div></div><div class=""><div style="margin: 0cm 0cm 0cm 36pt; font-size: 11pt; font-family: Calibri, sans-serif;" class=""> <o:p class=""></o:p></div></div><div class=""><div style="margin: 0cm 0cm 0cm 36pt; font-size: 11pt; font-family: Calibri, sans-serif;" class="">Gökhan<o:p class=""></o:p></div></div><div class=""><div style="margin: 0cm 0cm 0cm 36pt; font-size: 11pt; font-family: Calibri, sans-serif;" class=""> <o:p class=""></o:p></div></div><div style="margin: 0cm 0cm 0cm 36pt; font-size: 11pt; font-family: Calibri, sans-serif;" class=""><span style="font-size: 9pt; font-family: Helvetica, sans-serif;" class="">_______________________________________________<br class="">ChimeraX-users mailing list<br class=""></span><a href="mailto:ChimeraX-users@cgl.ucsf.edu" style="color: blue; text-decoration: underline;" class=""><span style="font-size: 9pt; font-family: Helvetica, sans-serif;" class="">ChimeraX-users@cgl.ucsf.edu</span></a><span style="font-size: 9pt; font-family: Helvetica, sans-serif;" class=""><br class="">Manage subscription:<br class=""></span><a href="https://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users" style="color: blue; text-decoration: underline;" class=""><span style="font-size: 9pt; font-family: Helvetica, sans-serif;" class="">https://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users</span></a><o:p class=""></o:p></div></div></blockquote></div><div style="margin: 0cm 0cm 0cm 36pt; font-size: 11pt; font-family: Calibri, sans-serif;" class=""><o:p class=""> </o:p></div></div></div></div></blockquote></div><br class=""></div></div></body></html>