March 2021 - ChimeraX-users - RBVI Mailing Lists

Surface dust command in the .cxc script
by 李泽 24 Feb '25

24 Feb '25

Hi all: I'm trying to use the .cxc script to run the software, I found that the "surface dust" command has never been executed in it. Have anyone met the same problem? Any suggestions. Thank you all. Best, Ze

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Get color code of a custom color
by Ahmad Khalifa 11 Feb '25

11 Feb '25

I created a custom color that I want to use in a different session. is there a way to do that besides trying to match colors by eye? Regards.

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Double and Triple Bond Stick Style
by Smith, Chase 05 Feb '25

05 Feb '25

Dear ChimeraX, I was just wondering why there is no way to represent a double or triple bond in either the ligands or the protein amino acids when viewing as a Stick or Ball-and-Stick representation? I sometimes use Chimera or ChimeraX to make visuals for my lectures, and the students often have difficulty in understanding due to the absence of the multiple bonds. I would love to have the ability to represent the double or triple bonds with multiple lines between the atoms. Thank you, Chase Smith ... ChaseSmith, PhD Chair, Department of Pharmaceutical Sciences & Associate Professor of Medicinal Chemistry School of Pharmacy MCPHS University 19 Foster Street | WorcesterMA01608 T 508.373.5717F 508.890.5618C 978.855.7203 chase.smith(a)mcphs.edu www.mcphs.edu MCPHS University Confidentiality Note: This e-mail, and any attachment to it, is intended to be confidential and might be legally privileged. It is intended solely for the use of the addressee. If you are not the intended recipient, you are hereby notified that reading, copying, disseminating or distributing this email is strictly prohibited. If you have received this e-mail in error, please immediately return it to the sender and delete it from your system. Thank you.

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Quest 2 Support?
by Blaine Hewitt 27 Dec '24

27 Dec '24

Hello, my name is Blaine Hewitt. Now I know that you have stated previously that you have no intention of bringing support to the Oculus Quest. Which is completely understandable since I know that not only would you have to develop around a completely new Operating System but another CPU architecture and much much more I assume. But with the soon release of the Oculus Quest 2 and it's new XR 2 chip-set makes a pretty good argument for it. As this would allow for much easier use in education (as is what I am attempting to do with it). I think it will be even easier now to push updates with SideQuest <https://sidequestvr.com/> being relatively simple to setup. I know that another (Naome <https://blog.matryx.ai/nanome-on-quest-public-beta-is-now-available-b546321…>) program is already available on the platform. But I do like your program a lot more since it is able to be used for free unlike Nanome Pricing <https://nanome.ai/pricing/> which is... as to say unappealing to public schools (such as mine). I was was also thinking (sorry if I am becoming annoying at this point) that if you do make a version of the Quest that you could make that GitHub branch available to the public. As for example while I may not be great at understanding complex protein structures I can help to make the whole experience more user friendly. Anyways if you read this far thank you for taking time from your day to read this. If you want to know who I am, my name is Blaine I am in my senior year of High School (Waynecsd <https://wh.waynecsd.org/>). I have to do a project by the end of the year where I have to present an area of study I want to pursue and I decided to research the effects of VR on the human's ability to learn and retain information. Budget..... None

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Apple silicon (M1 chip) native version?
by Jeffrey D. Hartgerink 28 Apr '22

28 Apr '22

Are there any plans for an Apple Silicon (M1 chip) native version of ChimeraX? While things work ok via the Rosetta emulator, it would be great to have the performance from a native app. -------------------------------------- Jeffrey D. Hartgerink, Ph.D. Prof. of Chemistry and Bioengineering Rice University, MS 602 6100 Main Street Houston, TX 77005 jdh(a)rice.edu / 713-348-4142 hartgerink.rice.edu

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How to Align Chromosome Models with Different Number of Atoms?
by Cardiff Jiang 30 Jul '21

30 Jul '21

Dear ChimeraX User List, How can I compare two chromosome 3D models (PDB files) that have different numbers of "atoms"? Matchmaker tool reports, "Reference and/or match model contains no nucleic or amino acid chains. Use the command-line 'align' command to superimpose small molecules/ligands." align #1 toAtoms #2 reports, "Unequal number of atoms to pair, 49 and 63." align #1 toAtoms #2 matchNumbering true reports, "Pairing dropped 49 atoms and 63 reference atoms. No atoms paired for alignment." align #1:1-40 to #2:1-40 reports, "No atoms paired for alignment." How should I compare two chromosome 3D models below? Thank you. [image: image.png] Best regards, Zichen "Cardiff" Jiang

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Re: [chimerax-users] Displaying silhouette around specific visual elements
by Tom Goddard 01 Apr '21

01 Apr '21

Hi Gustavo, Glad you noticed the smoothness of the surface. I made it smoother than the default. The surface came from the molmap command which computes a density map from the atomic model. That command uses a density map grid spacing of 1/3 the requested resolution by default, but I specified an extra option that used a grid spacing 1/8 of the resolution: open 2gbp molmap #1 8 gridSpacing 1 Also if you are doing this with a big molecule (100,000 atoms) the density map created may be very large and may be shown subsampled so the surface looks coarser. Make sure to set the "step" to 1 in the Volume Viewer panel so that it uses the full resolution of the computed map instead of step 2 which would use only every other grid point. One more pro tip about that image composition example. It only worked nicely because the atomic structure was completely behind the surface, so I could layer the surface on top. If part of the atomic model was behind and part in front (for example with a cryoEM map surface), then the layering would not work well -- the composite image would have the surface in front everywhere. Elaine's selection highlight approach can handle that situation with correct occlusions but the edging is not as nice as silhouettes. Tom > On Mar 31, 2021, at 1:00 PM, de Miranda Seabra, Gustavo <seabra(a)cop.ufl.edu> wrote: > > Hi Tom, > > This looks beautiful! Just one tangential question: How do you get such a smooth surface? Can you share the exact commands you gave? > > Thanks! > > -- > Gustavo Seabra > Assistant Scientist > Center for Natural Products, Drug Discovery and Development (CNPD3) > Department of Medicinal Chemistry > College of Pharmacy > University of Florida, Gainesville, FL, USA > From: ChimeraX-users <chimerax-users-bounces(a)cgl.ucsf.edu <mailto:chimerax-users-bounces@cgl.ucsf.edu>> on behalf of Tom Goddard <goddard(a)sonic.net <mailto:goddard@sonic.net>> > Sent: Tuesday, March 30, 2021 8:55 PM > To: Andre LB Ambrosio <andre(a)ifsc.usp.br <mailto:andre@ifsc.usp.br>> > Cc: ChimeraX Users Help <chimerax-users(a)cgl.ucsf.edu <mailto:chimerax-users@cgl.ucsf.edu>> > Subject: Re: [chimerax-users] Displaying silhouette around specific visual elements > > [External Email] > Hi Andre, > > If you are willing to go to a little trouble you can get silhouettes on an atomic model beneath a transparent surface that has no silhouettes. You first save an image of the atomic model with silhouettes with no surface, then save an image of the transparent surface with no atomic model and no silhouettes, then overlay the second image on the first in a photo editor like Gimp. Below is Elaine's example done this way. The command to save the surface image with transparency for overlaying is "save transpsurf.png transparentBackground true". > > Tom > > Overlay of two images. > > > Atomic model image > > > Transparent surface image > > >> On Mar 30, 2021, at 3:11 PM, Andre LB Ambrosio <andre(a)ifsc.usp.br <mailto:andre@ifsc.usp.br>> wrote: >> >> Dear Elaine, that is excellent! It is the visual effect I was looking for indeed. >> Thank you very much for this and thank you Tom for the very detailed response and for the feature request ticket. >> Andre. >> >> Em ter., 30 de mar. de 2021 às 15:59, Elaine Meng <meng(a)cgl.ucsf.edu <mailto:meng@cgl.ucsf.edu>> escreveu: >> Hi Andre, >> Sometimes you can approximately "fake" this effect by using the selection outline. It is not the same, however, as silhouettes; it will only go around the outside perimeter of the selected item(s). For example, if I have a molecule inside a map surface, I can make the surface transparent, select the atomic structure, and make the selection outline color black etc. as in these commands, resulting in the appearance in the attached image. >> >> open 2gbp >> molmap protein 8 >> trans 70 >> view >> set bgColor white >> select @* >> graphics selection color black >> >> I hope this helps, >> Elaine >> ----- >> Elaine C. Meng, Ph.D. >> UCSF Chimera(X) team >> Department of Pharmaceutical Chemistry >> University of California, San Francisco >> >> >> >> >>> On Mar 25, 2021, at 8:23 PM, Tom Goddard <goddard(a)sonic.net <mailto:goddard@sonic.net>> wrote: >>> >>> Hi Andre, >>> >>> It is not currently possible to display silhouettes on some models and not others. >>> >>> Several people have wanted this but I think it is complex to achieve. The silhouettes show boundaries where the depth in the entire scene changes abruptly. In order to have per-model silhouettes the ChimeraX GPU shader programs would need to compute an additional depth buffer separately for each model. Also the silhouette edges are not currently drawn at a specific depth. If per-model silhouettes were supported a stick model with silhouettes beneath a transparent surface needs to draw the silhouettes under the transparent surface so knowing the depth of the silhouette edge becomes important. When not using silhouettes the shader programs need to not compute the extra per-model depth buffers otherwise it would slow down rendering even when not being used. Adding these additional complexities to already complex graphics rendering shader programs have so far made this feature out of reach for our one graphics rendering developer (me). >>> >>> I made a feature request for per-model silhouette edges and perhaps in the future we will find a simpler way to implement it that makes it feasible. >>> >>> https://www.rbvi.ucsf.edu/trac/ChimeraX/ticket/4420 <https://urldefense.proofpoint.com/v2/url?u=https-3A__www.rbvi.ucsf.edu_trac…> >>> >>> Tom >>> >>>> On Mar 25, 2021, at 10:09 PM, Andre LB Ambrosio <andre(a)ifsc.usp.br <mailto:andre@ifsc.usp.br>> wrote: >>>> >>>> Dear all, >>>> >>>> I wonder if it's possible to display silhouettes selectively in the same figure; for instance, displaying silhouettes only on structure representation (around sticks, spheres, cartoons and so on), but not around the maps or volumes that surround them. >>>> Many thanks in advance, >>>> >>>> Andre >>>> _ >> >> >> -- >> Andre LB Ambrosio >> Associate Professor, IFSC/USP - Brazil >> www.ifsc.usp.br/alba <https://urldefense.proofpoint.com/v2/url?u=http-3A__www.ifsc.usp.br_alba&d=…> >> _______________________________________________ >> 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://urldefense.proofpoint.com/v2/url?u=https-3A__plato.cgl.ucsf.edu_mai…>

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Displaying silhouette around specific visual elements
by Andre LB Ambrosio 31 Mar '21

31 Mar '21

Dear all, I wonder if it's possible to display silhouettes selectively in the same figure; for instance, displaying silhouettes only on structure representation (around sticks, spheres, cartoons and so on), but not around the maps or volumes that surround them. Many thanks in advance, Andre

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Re: [chimerax-users] [Chimera-users] Debug
by 안예림 30 Mar '21

30 Mar '21

As soon as I start Chimera, the error message appears. I don't know how to report a bug to you. help me -----Original Message----- From: "Eric Pettersen"<pett(a)cgl.ucsf.edu> To: "안예림"<cp7617(a)naver.com>; Cc: <chimera-users(a)cgl.ucsf.edu>; Sent: 2021-03-30 (화) 03:36:23 (GMT+09:00) Subject: Re: [Chimera-users] Debug You should start Chimera and immediately use Help→Report A Bug to send a bug report to us, with a short description of the problem like you provided here. That will automatically provide us with many details about the machine you are using and the version of Chimera you are running. We can carry on from there, since I imagine this problem is only affecting you and therefore other people on this mailing list wouldn't want to get mail about all the details of this problem. --Eric Eric Pettersen UCSF Computer Graphics Lab On Mar 28, 2021, at 10:28 PM, 안예림 <cp7617(a)naver.com> wrote: Hi I have tried to make a movie of MD simulation by Chimera. I could be done one time, then for other MD’s it exits abnormally with the code -1073741819. Even I have decreased the size of .xtc file, it exits abnormally yet. Please check my capture picture. I have reinstalled chimera, but the problem did not resolve.What should I have to do ? I need your assistant. Thanksbe <20210329_142325.png>_______________________________________________ Chimera-users mailing list: Chimera-users(a)cgl.ucsf.edu Manage subscription: https://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users

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xchimera multiscale model
by Ana Sofia Ramos 29 Mar '21

29 Mar '21

Hi, I am having some difficulties in using xchimera, and I would like to ask you if you could help me. I want to make a representation of a virus-like nanoparticle using the pdb 1HQK. I have searched in the tutorial of xchimera but I could not find the general instructions, but I found them in the tutorial of chimera (multiscale model), however, the options are not present in my installation xchimera (and also in my installation of chimera). Then, I thought that maybe you could tell me how to make it in xchimera. Thank you very much for your attention. Kind regards, Ana

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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. 26 Mar '21

26 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 26 Mar '21

26 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 23 Mar '21

23 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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Move model to specific coordinates of reference model
by Vorländer,Matthias Kopano 19 Mar '21

19 Mar '21

Hi there, I am trying to place a model (volume) at specific coordinates of a second volume (the first model is a map and the second model is a tomogram). I have managed to place a sphere at the desired position, but I can’t figure out how do this with a volume file. Example for placing the sphere: shape sphere radius 100 center 5243.80,3103.88,1086.01 coordinateSystem #1 How can I achieve the same but placing a volume at the desired location? Thanks a lot, Best, Matthias

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building peptides in Chimera/ChimeraX
by Elaine Meng 18 Mar '21

18 Mar '21

Hello Ishita, Your question was forwarded. I'm CC'ing chimerax-users(a)cgl.ucsf.edu (which is the recommended address for asking ChimeraX questions, for future reference). Peptide-building in ChimeraX (and Chimera) does not predict the structure, it simply uses whatever angles you choose in the Build Structure tool. So the reason it looks like a helix is that you told it to use the helix phi,psi angles. ChimeraX build structure: <https://rbvi.ucsf.edu/chimerax/docs/user/tools/buildstructure.html#start> In the paper figure, it says that the indolicin structure is PDB 1g89 ... so if you want it to look like that, just open 1g89. In the legend it says structures generated by Chimera, but apparently they just mean that images of the structures (from the PDB) were generated by Chimera. 1g89 is an NMR ensemble of 16 structures, so they apparently just chose one of the structures to show and hid the others. I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco > -------- Forwarded Message -------- > Subject: Request regarding ChimeraX (From UC Davis) > Date: Wed, 17 Mar 2021 02:04:17 +0000 > From: Ishita M Shah <imshah(a)ucdavis.edu> > > Dear Dr. Ferrin, > I’m a Project Scientist at UC Davis and the newest user of ChimeraX. > I have a few questions regarding peptide secondary structure generation using ChimeraX. Would you please connect me to someone who could spare a few minutes to walk me through? > > Specifically, when I look up the secondary structure of Indolicidin (generated using Chimera) _ image attached from publication (it shows an extended structure), whereas, using Tools -> Structure editing -> Build Structure -> Start Structure -> Peptide/ Input sequence, the image I get is completely different (attached .bmp file). I really have basic requirements of prediction of secondary structures of peptides (and was using Indolicidin as an control) prior to exploring more. > > I apologize if this information regarding the use of ChimeraX for this purpose is readily available and that I could just be unaware of it. Any advice you can offer is highly appreciated. > > Best, > ishita. > > Ishita M. Shah, PhD > Associate Project Scientist > Associate Director, Microbial Programs > Foods for Health Institute > Department of Food Science and Technology > University of California Davis > 1221 Robert Mondavi Institute, South > Davis, CA 95616 > Phone: (530) 754-7962 > > https://ffhi.ucdavis.edu/people/ishita-shah > https://www.linkedin.com/in/ishita-m-shah-ph-d-a6a9664/ >

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Re: [chimerax-users] Global Diffusion Tensor Models
by Tom Goddard 17 Mar '21

17 Mar '21

Hi Arun, I see from the image you sent that the diffusion ellipsoid script I sent you gave the wrong ellipsoid orientation -- it was using the inverse of the rotation. Here is the correct ChimeraX script which I have also put on the ChimeraX Recipes web site: https://rbvi.github.io/chimerax-recipes/ellipsoid/ellipsoid.html <https://rbvi.github.io/chimerax-recipes/ellipsoid/ellipsoid.html> Tom > On Mar 17, 2021, at 12:23 PM, Gupta, Arun <Arun.Gupta(a)warwick.ac.uk> wrote: > > Dear Tom, > > I think this is what you referring w.r.t to orientation. I have also overlaid the ROTDIF generated output " Tensor axes " on the protein PDB in the attached pic. Although, the ellipsoid shape model representation doesn't looks great. > > Best Regards > > Arun >

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How to produce a multiple sequence alignment
by Luca Pellegrini 17 Mar '21

17 Mar '21

Hello, I have superposed several similar structures with Matchmaker, and now would like to obtain a structure-based multiple sequence alignment. In Chimera, Matchmaker has a nice button ‘After superposition, compute structure-based multiple sequence alignment’. ChimeraX produces all pairwise alignments with the reference structure, but how do I obtain a single alignment with all my sequences? Best wishes, Luca Luca Pellegrini, PhD Department of Biochemistry University of Cambridge Cambridge CB2 1GA UK

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Global Diffusion Tensor Models
by Gupta, Arun 17 Mar '21

17 Mar '21

Dear ChimeraX team, I am interested in generating Global diffusion tensor geometry models such as Prolate, Ellipsoid, Oblate or Sphere with overlaid protein PDB or structure of my interest. (As shown in attached pic). I am using diffusion tensor prediction module provided in ROTDIF software (http://gandalf.umd.edu/FushmanLab/pdsw.html) to generate an ellipsoid diffusion tensor of a protein molecule of my interest. Is it possible that I can use ROTDIF generated output (Which is in Pymol output format, please find attached ) to open in ChimeraX with my protein PDB, to render such representative figure ? Thanks!!! Arun Arun Gupta PhD, MRSC Research Fellow Challis & Lewandowski Group Chemistry Department University of Warwick Gibbet Hill Road Coventry CV4 7AL United Kingdom

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