March 2021 - ChimeraX-users - RBVI Mailing Lists

Rotate PDB file around euler angles in ChimeraX
by Vorländer,Matthias Kopano 26 Mar '21

26 Mar '21

Dear all, So, I am working with a tomogram and refined subtomogram average and would like fit all copies of the molecule, represented as a pdb file, back into the tomogram at all positions where it was found. In practice this means to translate the pdb file to specific coordinates of a reference volume (tomogram) and then rotate it around 3 euler angles defined in a relion star file. I figured out the translation part (thanks to your help), but for the rotation I could only find this script (https://plato.cgl.ucsf.edu/trac/chimera/attachment/wiki/Scripts/eulermove.py) for chimera which allows to rotate a volume around the euler angles and then resample the transformed volume and save it. While a workaround would be to do the operation with the volume in chimera, then fit the pdb file in the transformed volume, and then save the transformed pdb file, and then load everything back in chimera, the manual fitting of the pdb would become very laborious for several hundred copies. So ideally, I would like to adapt the eulermove.py script that I linked to i) work in ChimeraX and ii) work with pdbs instead of volumes. Unfortunately I have zero coding experience… Any help would be much appreciated! Best, Matthias

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RR distance maps
by William S Wang 26 Mar '21

26 Mar '21

Is there implementation of RR distance maps from chimera?

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generating icosahedron from pentamer
by Moustafa, Ibrahim M. 25 Mar '21

25 Mar '21

Dear all, I want to generate icosahedral structure from a pentamer (chains A-E). When I use the command: sym #1 i,222 coordinateSystem #2 center #2 It generated 5 copies, icosahedron for each chain. What I'd like to build is just 12 copies of the pentamer in an icosahedral sym. How to do that in ChimeraX? Thanks, Ibrahim

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Custom Palette
by Abhilash Padvannil 25 Mar '21

25 Mar '21

Hi, I am wondering if there is a way to create custom palettes for use in ChimeraX. Please suggest. Thanks Regards Abhilash.

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Making New Bonds between two molecules in ChimeraX
by Steven Truong 25 Mar '21

25 Mar '21

Dear ChimeraX Admins and Elaine, Hello, I was wondering if ChimeraX now has a “bond” command. I saw an inquiry like this in the mailing list archives (https://www.rbvi.ucsf.edu/pipermail/chimerax-users/2020-April/001029.html) but it seems like bond is still not an official functionality. When I switched over to Chimera and tried using the “bond” command, I get the error “Cannot form covalent bond joining two molecules,” even though I’ve saved all of the molecules into one PDB file. Is it because Chimera still sees these two sub-models as un-joinable? My command looks something like: "bond #0:61.A@ND2 #0.1:1222.X@C1”. For further context, we are trying to script orienting/bonding residues to glycans. We’ve been able to figure out aligning and orienting the glycans quite well with the scripts alone (.py scripts), but it seems like we’ll have to find another way to make bonds between the proteins/glycans. Do you have any suggestions? Ideally, we’d also keep as much of the pipeline in ChimeraX, but if it’s necessary, we could further pursue the ChimeraX+Chimera route. Thank you for your help! Many thanks, Steven Truong sdt45(a)cam.ac.uk<mailto:sdt45@cam.ac.uk> Cambridge University

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SwissSidechain equivalent for ChimeraX
by Madeline Grace Rollins 24 Mar '21

24 Mar '21

Hi all, I would like to mutate a serine residue to phosphoserine for one of the proteins I am working with. I have used SwissSidechain in Chimera to do this in the past, but I was wondering if there is an equivalent module like SwissSidechain but for ChimeraX? I tried downloading the SEQCROW bundle for structure editing, but I couldn't find the same range of sidechain derivatives. If not, can you use SwissSidechain in ChimeraX? I apologize in advance if this question has been asked already. Thank you, Madeline

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Questions about focal length of camera in ChimeraX
by Bin Shi 24 Mar '21

24 Mar '21

Thanks very much for your software so that I can specify the camera position and then take a snapshot. However, I can't find the information on the focal length of the virtual camera. I am using mono (default) – monoscopic with perspective (apparent size decreasing with distance from the viewer), and I didn't see any details about the camera intrinsics. Regards, Bin ----------------------------------------------------------------------------------------------- Department of Materials Science and Engineering, University of Toronto Email: binmse.shi(a)mail.utoronto.ca

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Re: [chimerax-users] VR Support
by Tom Goddard 24 Mar '21

24 Mar '21

Hi Gökhan, 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. https://www.theverge.com/2021/3/23/22345891/nvidia-amd-rtx-gpus-price-scalp… <https://www.theverge.com/2021/3/23/22345891/nvidia-amd-rtx-gpus-price-scalp…> 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. 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. Tom > On Mar 23, 2021, at 12:11 AM, <tolung.bio(a)gmail.com> <tolung.bio(a)gmail.com> wrote: > > Hi Tom, > > Thanks for the prompt response. > > My responses are below. > > Cheers, > > Gökhan > > > > From: Tom Goddard <goddard(a)sonic.net <mailto:goddard@sonic.net>> > Sent: Tuesday, 23 March 2021 5:49 PM > To: tolung.bio(a)gmail.com <mailto:tolung.bio@gmail.com> > Cc: Tristan Croll <tic20(a)cam.ac.uk <mailto:tic20@cam.ac.uk>>; ChimeraX Users Help <chimerax-users(a)cgl.ucsf.edu <mailto:chimerax-users@cgl.ucsf.edu>>; Simon Brown <simonb(a)uow.edu.au <mailto:simonb@uow.edu.au>>; James Bouwer <jbouwer(a)uow.edu.au <mailto:jbouwer@uow.edu.au>> > Subject: Re: [chimerax-users] VR Support > > Hi Gökhan, > > ISOLDE works in VR in a minimal way -- you can tug on atoms. Here's a little video showing that in ChimeraX 1.1. > > https://www.rbvi.ucsf.edu/chimerax/data/isolde-vr-mar2021/isolde_vr.mp4 <https://www.rbvi.ucsf.edu/chimerax/data/isolde-vr-mar2021/isolde_vr.mp4> > > 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. > > 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… > > 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. > > ABSOLUTELY, and I cannot wait for that day that I’ve been waiting for since I started working on structures, to come… > > 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. > > 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! > > 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? > > 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. > > 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. ☹ Does it work as well as ChimeraX+ISOLDE in refining models? > > Tom > > > > >> On Mar 22, 2021, at 9:18 PM, <tolung.bio(a)gmail.com <mailto:tolung.bio@gmail.com>> <tolung.bio(a)gmail.com <mailto:tolung.bio@gmail.com>> wrote: >> >> Hello Tristan and the Chimera team, >> >> I have been using ChimeraX in VR: fantastic! >> >> However, ISOLDE was not working in VR, unfortunately. >> >> Is there a fix/workaround currently available to get ISOLDE running in VR? >> >> Is there ongoing work on making ISOLDE VR compatible? >> >> 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. >> >> 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 😊). >> >> Best, >> >> Gökhan >> >> _______________________________________________ >> ChimeraX-users mailing list >> ChimeraX-users(a)cgl.ucsf.edu <mailto:ChimeraX-users@cgl.ucsf.edu> >> Manage subscription: >> https://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users <https://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users> >

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Re: [chimerax-users] movie in ChimeraX
by Elaine Meng 24 Mar '21

24 Mar '21

> On Mar 23, 2021, at 5:04 AM, Ruchika Bajaj <phd.ruchika(a)gmail.com> wrote: > > Hi Elaine > I am trying to figure out two things. Could you please help me with this? I would appreciate your help. > 1. I have two structures. The first one doesn't have a ligand and the second one has two ligands. I am trying to make a movie with these steps. 1) first structure, 2) two ligands are coming or flying in the picture, 3) then the 2nd structure with two ligands. However, when I am trying to make the morph between the first and second structure, it doesn't show any ligand. I did check the following link, where it discusses that both structures should have ligands to include it in the morph. So, my question is how should I include the ligand ? Could you please explain me with command usage? Thanks !! > <http://rbvi.ucsf.edu/chimerax/docs/user/commands/morph.html#pairing> > 2. I heard that frames/sec rate could be increased to smoothen steps in movies. I checked the maxFrameRate command. However, I don't know the usage. Could you please help me with that ? > Thanks a lot for your help !! Your prompt response would help me to proceed further. > Regards > Ruchika Hi Ruchika, Please send questions to chimerax-users(a)cgl.ucsf.edu (if you are using ChimeraX) or chimera-users(a)cgl.ucsf.edu (if using Chimera) rather than my individual address, or else they may not get answered. (1) as explained here <https://rbvi.ucsf.edu/chimerax/docs/user/commands/morph.html#pairing> morph only contains the atoms that are the same in both start and end structures. You can show ligands but because they are not included in the morph model, you have to display the ligand(s) from the original model (or an additional copy of the original model) along with the protein in the morph model. Moving them to different positions is even more complicated than showing/hiding. There is a Chimera tutorial that covers this, and what you would do with ChimeraX is similar except that ChimeraX "view" is used to save and restore positions instead of the Chimera commands "savepos" and "reset": <https://www.rbvi.ucsf.edu/chimera/data/tutorials/movies08/moviemaking.html> (2) if you mean you want more steps in the morph (more gradual change) then you would use the "frames" option in the morph command. Probably that is what you want. <https://rbvi.ucsf.edu/chimerax/docs/user/commands/morph.html#top> However, if you really mean you wanted movie framerate, then it is the "framerate" option of the "movie encode" command. <https://rbvi.ucsf.edu/chimerax/docs/user/commands/movie.html#encode> I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco

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VR Support
by tolung.bio＠gmail.com 22 Mar '21

22 Mar '21

Hello Tristan and the Chimera team, I have been using ChimeraX in VR: fantastic! However, ISOLDE was not working in VR, unfortunately. Is there a fix/workaround currently available to get ISOLDE running in VR? Is there ongoing work on making ISOLDE VR compatible? 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. 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 😊). Best, Gökhan

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